Skip to content

GitLab

Commit 82a82741 authored by peastman's avatar peastman
Browse files

Merge pull request #1076 from swails/tests 

Add a set of unit tests for unit handling in the core API.
parents 9b240457 e585fb6e
Hide whitespace changes
Inline Side-by-side
Showing with 1322 additions and 34 deletions
devtools/forcefield-scripts/processTinkerForceField.py
View file @ 82a82741
...@@ -1017,7 +1017,6 @@ if( isAmoeba ): ...@@ -1017,7 +1017,6 @@ if( isAmoeba ):
torsionTorsionUnit = 1.0 torsionTorsionUnit = 1.0
outputString = """ <AmoebaTorsionTorsionForce >""" outputString = """ <AmoebaTorsionTorsionForce >"""
tinkerXmlFile.write( "%s\n" % (outputString ) ) tinkerXmlFile.write( "%s\n" % (outputString ) )
conversion = 41.84/radian
torsionTorsions = forces['tortors'] torsionTorsions = forces['tortors']
for (index, torsionTorsion) in enumerate(torsionTorsions): for (index, torsionTorsion) in enumerate(torsionTorsions):
torInfo = torsionTorsion[0] torInfo = torsionTorsion[0]
......
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 82a82741
...@@ -127,7 +127,7 @@ public: ...@@ -127,7 +127,7 @@ public:
* @param particle1 the index of the first particle connected by the angle * @param particle1 the index of the first particle connected by the angle
* @param particle2 the index of the second particle connected by the angle * @param particle2 the index of the second particle connected by the angle
* @param particle3 the index of the third particle connected by the angle * @param particle3 the index of the third particle connected by the angle
* @param length the angle measured in degrees * @param length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
* @return the index of the angle that was added * @return the index of the angle that was added
*/ */
...@@ -140,7 +140,7 @@ public: ...@@ -140,7 +140,7 @@ public:
* @param particle1 the index of the first particle connected by the angle * @param particle1 the index of the first particle connected by the angle
* @param particle2 the index of the second particle connected by the angle * @param particle2 the index of the second particle connected by the angle
* @param particle3 the index of the third particle connected by the angle * @param particle3 the index of the third particle connected by the angle
* @param length the equilibrium angle, measured in degress * @param length the equilibrium angle, measured in degrees
* @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2 * @param quadratic k the quadratic force constant for the angle, measured in kJ/mol/radian^2
*/ */
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK) const; void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h
View file @ 82a82741
...@@ -74,7 +74,7 @@ public: ...@@ -74,7 +74,7 @@ public:
* *
* @return global cubicK term * @return global cubicK term
*/ */
double getAmoebaGlobalOutOfPlaneBendCubic(void) const; double getAmoebaGlobalOutOfPlaneBendCubic() const;
/** /**
* Set the global cubic term * Set the global cubic term
...@@ -88,7 +88,7 @@ public: ...@@ -88,7 +88,7 @@ public:
* *
* @return global quartic term * @return global quartic term
*/ */
double getAmoebaGlobalOutOfPlaneBendQuartic(void) const; double getAmoebaGlobalOutOfPlaneBendQuartic() const;
/** /**
* Set the global pentic term * Set the global pentic term
...@@ -102,7 +102,7 @@ public: ...@@ -102,7 +102,7 @@ public:
* *
* @return global penticK term * @return global penticK term
*/ */
double getAmoebaGlobalOutOfPlaneBendPentic(void) const; double getAmoebaGlobalOutOfPlaneBendPentic() const;
/** /**
* Set the global sextic term * Set the global sextic term
...@@ -116,7 +116,7 @@ public: ...@@ -116,7 +116,7 @@ public:
* *
* @return global sexticK term * @return global sexticK term
*/ */
double getAmoebaGlobalOutOfPlaneBendSextic(void) const; double getAmoebaGlobalOutOfPlaneBendSextic() const;
/** /**
* Add an out-of-plane bend term to the force field. * Add an out-of-plane bend term to the force field.
......
wrappers/python/src/swig_doxygen/swigInputBuilder.py
View file @ 82a82741
...@@ -10,6 +10,7 @@ import getopt ...@@ -10,6 +10,7 @@ import getopt
import re import re
import xml.etree.ElementTree as etree import xml.etree.ElementTree as etree
from distutils.version import LooseVersion from distutils.version import LooseVersion
import copy
try: try:
from html.parser import HTMLParser from html.parser import HTMLParser
...@@ -20,7 +21,6 @@ except ImportError: ...@@ -20,7 +21,6 @@ except ImportError:
INDENT = " " INDENT = " "
docTags = {'emphasis':'i', 'bold':'b', 'itemizedlist':'ul', 'listitem':'li', 'preformatted':'pre', 'computeroutput':'tt', 'subscript':'sub'} docTags = {'emphasis':'i', 'bold':'b', 'itemizedlist':'ul', 'listitem':'li', 'preformatted':'pre', 'computeroutput':'tt', 'subscript':'sub'}
def striphtmltags(s): def striphtmltags(s):
"""Strip a couple html tags used inside docstrings in the C++ source """Strip a couple html tags used inside docstrings in the C++ source
to produce something more easily read as plain text. to produce something more easily read as plain text.
...@@ -157,7 +157,7 @@ class SwigInputBuilder: ...@@ -157,7 +157,7 @@ class SwigInputBuilder:
skipAdditionalMethods=[], skipAdditionalMethods=[],
SWIG_VERSION='3.0.2'): SWIG_VERSION='3.0.2'):
self.nodeByID={} self.nodeByID={}
self.SWIG_COMPACT_ARGUMENTS = LooseVersion(SWIG_VERSION) < LooseVersion('3.0.6') self.SWIG_COMPACT_ARGUMENTS = LooseVersion(SWIG_VERSION) < LooseVersion('3.0.5')
self.configModule = __import__(os.path.splitext(configFilename)[0]) self.configModule = __import__(os.path.splitext(configFilename)[0])
...@@ -477,7 +477,7 @@ class SwigInputBuilder: ...@@ -477,7 +477,7 @@ class SwigInputBuilder:
valueUnits=[None, ()] valueUnits=[None, ()]
index=0 index=0
if valueUnits[0]: if valueUnits[0] is not None:
sys.stdout.write("%s.%s() returns %s\n" % sys.stdout.write("%s.%s() returns %s\n" %
(shortClassName, methName, valueUnits[0])) (shortClassName, methName, valueUnits[0]))
if len(valueUnits[1])>0: if len(valueUnits[1])>0:
...@@ -491,10 +491,10 @@ class SwigInputBuilder: ...@@ -491,10 +491,10 @@ class SwigInputBuilder:
% (addText, INDENT, valueUnits[0]) % (addText, INDENT, valueUnits[0])
for vUnit in valueUnits[1]: for vUnit in valueUnits[1]:
if vUnit!=None: if vUnit is not None:
addText = "%s%sval[%s]=unit.Quantity(val[%s], %s)\n" \ addText = "%s%sval[%s]=unit.Quantity(val[%s], %s)\n" \
% (addText, INDENT, index, index, vUnit) % (addText, INDENT, index, index, vUnit)
index+=1 index+=1
if key in self.configModule.STEAL_OWNERSHIP: if key in self.configModule.STEAL_OWNERSHIP:
for argNum in self.configModule.STEAL_OWNERSHIP[key]: for argNum in self.configModule.STEAL_OWNERSHIP[key]:
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 82a82741
...@@ -216,22 +216,22 @@ UNITS = { ...@@ -216,22 +216,22 @@ UNITS = {
("AmoebaGeneralizedKirkwoodForce", "getDielectricOffset") : ( 'unit.nanometer', ()), ("AmoebaGeneralizedKirkwoodForce", "getDielectricOffset") : ( 'unit.nanometer', ()),
("AmoebaGeneralizedKirkwoodForce", "getIncludeCavityTerm") : ( None,()), ("AmoebaGeneralizedKirkwoodForce", "getIncludeCavityTerm") : ( None,()),
("AmoebaGeneralizedKirkwoodForce", "getProbeRadius") : ( 'unit.nanometer', ()), ("AmoebaGeneralizedKirkwoodForce", "getProbeRadius") : ( 'unit.nanometer', ()),
("AmoebaGeneralizedKirkwoodForce", "getSurfaceAreaFactor") : ( '(unit.nanometer*unit.nanometer)/unit.kilojoule_per_mole',()), ("AmoebaGeneralizedKirkwoodForce", "getSurfaceAreaFactor") : ( 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)',()),
("AmoebaAngleForce", "getAmoebaGlobalAngleCubic") : ( None,()), ("AmoebaAngleForce", "getAmoebaGlobalAngleCubic") : ( '1/unit.radian',()),
("AmoebaAngleForce", "getAmoebaGlobalAngleQuartic") : ( None,()), ("AmoebaAngleForce", "getAmoebaGlobalAngleQuartic") : ( '1/unit.radian**2',()),
("AmoebaAngleForce", "getAmoebaGlobalAnglePentic") : ( None,()), ("AmoebaAngleForce", "getAmoebaGlobalAnglePentic") : ( '1/unit.radian**3',()),
("AmoebaAngleForce", "getAmoebaGlobalAngleSextic") : ( None,()), ("AmoebaAngleForce", "getAmoebaGlobalAngleSextic") : ( '1/unit.radian**4',()),
("AmoebaAngleForce", "getAngleParameters") : ( None, (None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')), ("AmoebaAngleForce", "getAngleParameters") : ( None, (None, None, None, 'unit.degree', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaBondForce", "getAmoebaGlobalBondCubic") : ( None,()), ("AmoebaBondForce", "getAmoebaGlobalBondCubic") : ( '1/unit.nanometer',()),
("AmoebaBondForce", "getAmoebaGlobalBondQuartic") : ( None,()), ("AmoebaBondForce", "getAmoebaGlobalBondQuartic") : ( '1/unit.nanometer**2',()),
("AmoebaBondForce", "getBondParameters") : ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')), ("AmoebaBondForce", "getBondParameters") : ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleCubic") : ( None,()), ("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleCubic") : ( '1/unit.radian',()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleQuartic") : ( None,()), ("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleQuartic") : ( '1/unit.radian**2',()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAnglePentic") : ( None,()), ("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAnglePentic") : ( '1/unit.radian**3',()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleSextic") : ( None,()), ("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleSextic") : ( '1/unit.radian**4',()),
("AmoebaInPlaneAngleForce", "getAngleParameters") : ( None, (None, None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')), ("AmoebaInPlaneAngleForce", "getAngleParameters") : ( None, (None, None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaMultipoleForce", "getNumMultipoles") : ( None,()), ("AmoebaMultipoleForce", "getNumMultipoles") : ( None,()),
...@@ -256,7 +256,9 @@ UNITS = { ...@@ -256,7 +256,9 @@ UNITS = {
# void getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms ) # void getCovalentMap(int index, CovalentType typeId, std::vector<int>& covalentAtoms )
# void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists ) # void getCovalentMaps(int index, std::vector < std::vector<int> >& covalentLists )
("AmoebaMultipoleForce", "getMultipoleParameters") : ( None, ()), ("AmoebaMultipoleForce", "getMultipoleParameters") : ( None, ('unit.elementary_charge', 'unit.elementary_charge/unit.nanometer',
'unit.elementary_charge/unit.nanometer**2', None, None, None, None, None, None,
'unit.nanometer**3')),
("AmoebaMultipoleForce", "getCovalentMap") : ( None, ()), ("AmoebaMultipoleForce", "getCovalentMap") : ( None, ()),
("AmoebaMultipoleForce", "getCovalentMaps") : ( None, ()), ("AmoebaMultipoleForce", "getCovalentMaps") : ( None, ()),
("AmoebaMultipoleForce", "getScalingDistanceCutoff") : ( 'unit.nanometer', ()), ("AmoebaMultipoleForce", "getScalingDistanceCutoff") : ( 'unit.nanometer', ()),
...@@ -268,17 +270,17 @@ UNITS = { ...@@ -268,17 +270,17 @@ UNITS = {
("AmoebaMultipoleForce", "getSystemMultipoleMoments") : ( None, ()), ("AmoebaMultipoleForce", "getSystemMultipoleMoments") : ( None, ()),
("AmoebaOutOfPlaneBendForce", "getNumOutOfPlaneBends") : ( None, ()), ("AmoebaOutOfPlaneBendForce", "getNumOutOfPlaneBends") : ( None, ()),
("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendCubic") : ( None,()), ("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendCubic") : ( '1/unit.radian',()),
("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendQuartic") : ( None,()), ("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendQuartic") : ( '1/unit.radian**2',()),
("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendPentic") : ( None,()), ("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendPentic") : ( '1/unit.radian**3',()),
("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendSextic") : ( None,()), ("AmoebaOutOfPlaneBendForce", "getAmoebaGlobalOutOfPlaneBendSextic") : ( '1/unit.radian**4',()),
("AmoebaOutOfPlaneBendForce", "getOutOfPlaneBendParameters") : ( None, (None, None, None, None, 'unit.kilojoule_per_mole')), ("AmoebaOutOfPlaneBendForce", "getOutOfPlaneBendParameters") : ( None, (None, None, None, None, 'unit.kilojoule_per_mole/unit.radians**2')),
("AmoebaPiTorsionForce", "getNumPiTorsions") : ( None, ()), ("AmoebaPiTorsionForce", "getNumPiTorsions") : ( None, ()),
("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/unit.degree', 'unit.kilojoule_per_mole/unit.nanometer/unit.degree')), ("AmoebaStretchBendForce", "getStretchBendParameters") : ( None, (None, None, None, 'unit.nanometer', 'unit.nanometer', 'unit.radian', 'unit.kilojoule_per_mole/unit.nanometer/unit.radian', 'unit.kilojoule_per_mole/unit.nanometer/unit.radian')),
("AmoebaTorsionTorsionForce", "getNumTorsionTorsions") : ( None, ()), ("AmoebaTorsionTorsionForce", "getNumTorsionTorsions") : ( None, ()),
("AmoebaTorsionTorsionForce", "getNumTorsionTorsionGrids") : ( None, ()), ("AmoebaTorsionTorsionForce", "getNumTorsionTorsionGrids") : ( None, ()),
...@@ -376,6 +378,9 @@ UNITS = { ...@@ -376,6 +378,9 @@ UNITS = {
("CustomTorsionForce", "getPerTorsionParameterName") : (None, ()), ("CustomTorsionForce", "getPerTorsionParameterName") : (None, ()),
("CustomTorsionForce", "getGlobalParameterName") : (None, ()), ("CustomTorsionForce", "getGlobalParameterName") : (None, ()),
("CustomTorsionForce", "getTorsionParameters") : (None, ()), ("CustomTorsionForce", "getTorsionParameters") : (None, ()),
("DrudeForce", "getParticleParameters") : (None, (None, None, None, None, None, 'unit.elementary_charge', 'unit.nanometer**3', None, None)),
("DrudeForce", "getNumScreenedPairs") : (None, ()),
("DrudeForce", "getScreenedPairParameters") : (None, ()),
("GBSAOBCForce", "getParticleParameters") ("GBSAOBCForce", "getParticleParameters")
: (None, ('unit.elementary_charge', : (None, ('unit.elementary_charge',
'unit.nanometer', None)), 'unit.nanometer', None)),
......
wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i
View file @ 82a82741
...@@ -2,9 +2,10 @@ ...@@ -2,9 +2,10 @@
try: try:
import numpy import numpy
except: except ImportError:
pass numpy = None
import copy
import sys import sys
import math import math
RMIN_PER_SIGMA=math.pow(2, 1/6.0) RMIN_PER_SIGMA=math.pow(2, 1/6.0)
...@@ -224,3 +225,70 @@ class State(_object): ...@@ -224,3 +225,70 @@ class State(_object):
self._system = args[0] self._system = args[0]
self._integrator = args[1] self._integrator = args[1]
%} %}
%pythonprepend OpenMM::AmoebaAngleForce::addAngle %{
try:
length = args[3]
if isinstance(args, tuple):
args = list(args)
except (NameError, UnboundLocalError):
if unit.is_quantity(length):
length = length.value_in_unit(unit.degree)
else:
if unit.is_quantity(length):
args[3] = length.value_in_unit(unit.degree)
%}
%pythonprepend OpenMM::AmoebaAngleForce::setAngleParameters %{
try:
length = args[4]
if isinstance(args, tuple):
args = list(args)
except (NameError, UnboundLocalError):
if unit.is_quantity(length):
length = length.value_in_unit(unit.degree)
else:
if unit.is_quantity(length):
args[4] = length.value_in_unit(unit.degree)
%}
%pythonprepend OpenMM::AmoebaTorsionTorsionForce::setTorsionTorsionGrid %{
def deunitize_grid(grid):
if isinstance(grid, tuple):
grid = list(grid)
for i, row in enumerate(grid):
if isinstance(row, tuple):
row = list(row)
grid[i] = row
for i, column in enumerate(row):
if isinstance(column, tuple):
column = list(column)
row[i] = column
# Data is angle, angle, energy, de/dang1, de/dang2, d^2e/dang1dang2
if unit.is_quantity(column[0]):
column[0] = column[0].value_in_unit(unit.degree)
if unit.is_quantity(column[1]):
column[1] = column[1].value_in_unit(unit.degree)
if unit.is_quantity(column[2]):
column[2] = column[2].value_in_unit(unit.kilojoule_per_mole)
if len(column) > 3 and unit.is_quantity(column[3]):
column[3] = column[3].value_in_unit(unit.kilojoule_per_mole/unit.radians)
if len(column) > 4 and unit.is_quantity(column[4]):
column[4] = column[4].value_in_unit(unit.kilojoule_per_mole/unit.radians)
if len(column) > 5 and unit.is_quantity(column[5]):
column[5] = column[5].value_in_unit(unit.kilojoule_per_mole/unit.radians**2)
return grid
try:
grid = copy.deepcopy(args[1])
if isinstance(args, tuple):
args = list(args)
except (NameError, UnboundLocalError):
try:
# Support numpy arrays
grid = grid.tolist()
except AttributeError:
grid = copy.deepcopy(grid)
grid = deunitize_grid(grid)
else:
args[1] = deunitize_grid(grid)
%}
wrappers/python/tests/TestAPIUnits.py 0 → 100644
View file @ 82a82741
from __future__ import division
import unittest
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
import random
import math
class TestAPIUnits(unittest.TestCase):
"""Test the Simulation class"""
def assertAlmostEqualUnit(self, x1, x2):
self.assertAlmostEqual(x1._value, x2.value_in_unit(x1.unit))
def assertAlmostEqualUnitArray(self, a1, a2):
for x1, x2 in zip(a1._value, a2.value_in_unit(a1.unit)):
self.assertAlmostEqual(x1, x2)
def testHarmonicBondForce(self):
""" Tests HarmonicBondForce API features """
force = HarmonicBondForce()
force.addBond(0, 1, 1.0, 1.0)
force.addBond(2, 3, 1.0*angstroms,
1.0*kilocalories_per_mole/angstroms**2)
i, j, length, K = force.getBondParameters(0)
self.assertEqual(force.getNumBonds(), 2)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(length, 1.0*nanometers)
self.assertEqual(K, 1*kilojoules_per_mole/nanometers**2)
self.assertIs(length.unit, nanometers)
self.assertIs(K.unit, kilojoules_per_mole/nanometers**2)
i, j, length, K = force.getBondParameters(1)
self.assertEqual(i, 2)
self.assertEqual(j, 3)
self.assertEqual(length, 1.0*angstroms)
self.assertAlmostEqualUnit(K, 1*kilocalories_per_mole/angstroms**2)
self.assertIs(length.unit, nanometers)
self.assertIs(K.unit, kilojoules_per_mole/nanometers**2)
def testHarmonicAngleForce(self):
""" Tests HarmonicAngleForce API features """
force = HarmonicAngleForce()
force.addAngle(0, 1, 2, 180*degrees,
1.0*kilocalories_per_mole/radians**2)
force.addAngle(1, 2, 3, math.pi/2, 1.0)
self.assertEqual(force.getNumAngles(), 2)
i, j, k, angle, K = force.getAngleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(angle, 180*degrees)
self.assertEqual(K, 1.0*kilocalories_per_mole/radians**2)
self.assertIs(angle.unit, radians)
self.assertIs(K.unit, kilojoules_per_mole/radians**2)
i, j, k, angle, K = force.getAngleParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(angle, math.pi/2*radians)
self.assertEqual(K, 1.0*kilojoules_per_mole/radians**2)
self.assertIs(angle.unit, radians)
self.assertIs(K.unit, kilojoules_per_mole/radians**2)
def testPeriodicTorsionForce(self):
""" Tests PeriodicTorsionForce API features """
force = PeriodicTorsionForce()
force.addTorsion(0, 1, 2, 3, 1, math.pi, 1)
force.addTorsion(1, 2, 3, 4, 2, 180*degrees, 1*kilocalories_per_mole)
self.assertEqual(force.getNumTorsions(), 2)
i, j, k, l, per, phase, K = force.getTorsionParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(per, 1)
self.assertFalse(is_quantity(per))
self.assertEqual(phase, math.pi*radians)
self.assertEqual(K, 1*kilojoules_per_mole)
self.assertIs(phase.unit, radians)
self.assertIs(K.unit, kilojoules_per_mole)
i, j, k, l, per, phase, K = force.getTorsionParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertEqual(per, 2)
self.assertFalse(is_quantity(per))
self.assertEqual(phase, 180*degrees)
self.assertEqual(K, 1*kilocalories_per_mole)
self.assertIs(phase.unit, radians)
self.assertIs(K.unit, kilojoules_per_mole)
def testRBTorsionForce(self):
""" Tests the RBTorsionForce API features """
force = RBTorsionForce()
force.addTorsion(0, 1, 2, 3, 1, 2, 3, 4, 5, 6)
force.addTorsion(1, 2, 3, 4, 1*kilocalories_per_mole,
2*kilocalories_per_mole, 3*kilocalories_per_mole,
4*kilocalories_per_mole, 5*kilocalories_per_mole,
6*kilocalories_per_mole)
self.assertEqual(force.getNumTorsions(), 2)
i, j, k, l, c0, c1, c2, c3, c4, c5 = force.getTorsionParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(c0, 1*kilojoules_per_mole)
self.assertEqual(c1, 2*kilojoules_per_mole)
self.assertEqual(c2, 3*kilojoules_per_mole)
self.assertEqual(c3, 4*kilojoules_per_mole)
self.assertEqual(c4, 5*kilojoules_per_mole)
self.assertEqual(c5, 6*kilojoules_per_mole)
self.assertIs(c0.unit, kilojoules_per_mole)
self.assertIs(c1.unit, kilojoules_per_mole)
self.assertIs(c2.unit, kilojoules_per_mole)
self.assertIs(c3.unit, kilojoules_per_mole)
self.assertIs(c4.unit, kilojoules_per_mole)
self.assertIs(c5.unit, kilojoules_per_mole)
i, j, k, l, c0, c1, c2, c3, c4, c5 = force.getTorsionParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertAlmostEqualUnit(c0, 1*kilocalories_per_mole)
self.assertAlmostEqualUnit(c1, 2*kilocalories_per_mole)
self.assertAlmostEqualUnit(c2, 3*kilocalories_per_mole)
self.assertAlmostEqualUnit(c3, 4*kilocalories_per_mole)
self.assertAlmostEqualUnit(c4, 5*kilocalories_per_mole)
self.assertAlmostEqualUnit(c5, 6*kilocalories_per_mole)
self.assertIs(c0.unit, kilojoules_per_mole)
self.assertIs(c1.unit, kilojoules_per_mole)
self.assertIs(c2.unit, kilojoules_per_mole)
self.assertIs(c3.unit, kilojoules_per_mole)
self.assertIs(c4.unit, kilojoules_per_mole)
self.assertIs(c5.unit, kilojoules_per_mole)
def testNonbondedForce(self):
""" Tests the NonbondedForce API features """
force = NonbondedForce()
force.addParticle(1.0, 1.0, 1.0)
force.addParticle(1.0*coulombs, 1.0*angstroms,
1.0*kilocalories_per_mole)
self.assertEqual(force.getNumParticles(), 2)
charge, sigma, epsilon = force.getParticleParameters(0)
self.assertEqual(charge, 1.0*elementary_charge)
self.assertEqual(sigma, 1.0*nanometers)
self.assertEqual(epsilon, 1.0*kilojoules_per_mole)
self.assertIs(charge.unit, elementary_charge)
self.assertIs(sigma.unit, nanometers)
self.assertIs(epsilon.unit, kilojoules_per_mole)
charge, sigma, epsilon = force.getParticleParameters(1)
self.assertEqual(charge, 1.0*coulombs)
self.assertEqual(sigma, 1.0*angstroms)
self.assertEqual(epsilon, 1.0*kilocalories_per_mole)
self.assertIs(charge.unit, elementary_charge)
self.assertIs(sigma.unit, nanometers)
self.assertIs(epsilon.unit, kilojoules_per_mole)
force.setCutoffDistance(10*angstroms)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
force.setCutoffDistance(1)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
force.setSwitchingDistance(8*angstroms)
self.assertEqual(force.getSwitchingDistance(), 0.8*nanometers)
self.assertIs(force.getSwitchingDistance().unit, nanometer)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(NonbondedForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(NonbondedForce.CutoffNonPeriodic)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(NonbondedForce.CutoffPeriodic)
self.assertTrue(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(NonbondedForce.Ewald)
self.assertTrue(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(NonbondedForce.PME)
self.assertTrue(force.usesPeriodicBoundaryConditions())
def testCmapForce(self):
""" Tests the CMAPTorsionForce API features """
map1 = [random.random() for i in range(24*24)]
map2 = [random.random() for i in range(12*12)] * kilocalories_per_mole
force = CMAPTorsionForce()
force.addMap(24, map1)
force.addMap(12, map2)
force.addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4)
force.addTorsion(1, 5, 6, 7, 8, 6, 7, 8, 9)
force.addTorsion(0, 10, 11, 12, 13, 11, 12, 13, 14)
force.addTorsion(1, 15, 16, 17, 18, 16, 17, 18, 19)
self.assertEqual(force.getNumTorsions(), 4)
self.assertEqual(force.getNumMaps(), 2)
self.assertEqual(force.getMapParameters(0)[0], 24)
self.assertEqual(force.getMapParameters(1)[0], 12)
self.assertIs(force.getMapParameters(0)[1].unit, kilojoules_per_mole)
self.assertIs(force.getMapParameters(1)[1].unit, kilojoules_per_mole)
for x, y in zip(force.getMapParameters(0)[1], map1):
self.assertAlmostEqual(x.value_in_unit(kilojoules_per_mole), y)
for x, y in zip(force.getMapParameters(1)[1], map2):
self.assertAlmostEqualUnit(x, y)
def testCustomBondForce(self):
""" Tests the CustomBondForce API features """
force = CustomBondForce('1/2*k*(r-r0)^2')
force.addPerBondParameter('r0')
force.addBond(0, 1, [0.1])
force.addBond(1, 2, [1.0*angstroms])
self.assertEqual(force.getNumBonds(), 2)
i, j, req = force.getBondParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(req[0], 0.1)
i, j, req = force.getBondParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(req[0], 0.1)
def testCustomAngleForce(self):
""" Tests the CustomAngleForce API features """
force = CustomAngleForce('1/2*k*(theta-theta0)^2')
force.addPerAngleParameter('theta0')
force.addAngle(0, 1, 2, [math.pi / 2])
force.addAngle(3, 4, 5, [90*degrees])
self.assertEqual(force.getNumAngles(), 2)
i, j, k, theta = force.getAngleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(theta[0], math.pi / 2)
i, j, k, theta = force.getAngleParameters(1)
self.assertEqual(i, 3)
self.assertEqual(j, 4)
self.assertEqual(k, 5)
self.assertEqual(theta[0], math.pi / 2)
def testCustomTorsionForce(self):
""" Tests the CustomTorsionForce API features """
force = CustomTorsionForce('1/2*k*(theta-theta0)^2')
force.addTorsion(0, 1, 2, 3, [math.pi])
force.addTorsion(4, 5, 6, 7, [180*degrees])
self.assertEqual(force.getNumTorsions(), 2)
i, j, k, l, theta = force.getTorsionParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(theta[0], math.pi)
i, j, k, l, theta = force.getTorsionParameters(1)
self.assertEqual(i, 4)
self.assertEqual(j, 5)
self.assertEqual(k, 6)
self.assertEqual(l, 7)
self.assertEqual(theta[0], math.pi)
def testCustomCompoundBondForce(self):
""" Tests the CustomCompoundBondForce API features """
force = CustomCompoundBondForce(4, 'kb*distance(p1, p2)*distance(p2, p3)*distance(p3, p4)+'
'ka*angle(p1, p2, p3)*angle(p2, p3, p4)+'
'kd*dihedral(p1, p2, p3, p4)')
force.addPerBondParameter('kb')
force.addPerBondParameter('ka')
force.addPerBondParameter('kd')
force.addBond([0, 1, 2, 3], [1.0, 2.0, 3.0])
force.addBond([4, 5, 6, 7], [1.0*kilocalories_per_mole/angstroms,
2.0*kilocalories_per_mole/radians,
3.0*kilocalories_per_mole]
)
self.assertEqual(force.getNumBonds(), 2)
(i, j, k, l), (kb, ka, kd) = force.getBondParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(kb, 1)
self.assertEqual(ka, 2)
self.assertEqual(kd, 3)
(i, j, k, l), (kb, ka, kd) = force.getBondParameters(1)
self.assertEqual(i, 4)
self.assertEqual(j, 5)
self.assertEqual(k, 6)
self.assertEqual(l, 7)
self.assertEqual(kb, 1*10*4.184)
self.assertEqual(ka, 2*4.184)
self.assertEqual(kd, 3*4.184)
def testCustomExternalForce(self):
""" Tests the CustomExternalForce API features """
force = CustomExternalForce('1/2*k*k2*((x-x0)^2+(y-y0)^2+(z-z0)^2)')
force.addGlobalParameter('k', 10*kilocalories_per_mole/angstroms**2)
force.addGlobalParameter('k2', 20)
force.addPerParticleParameter('x0')
force.addPerParticleParameter('y0')
force.addPerParticleParameter('z0')
force.addParticle(0, [1.0, 2.0, 3.0])
force.addParticle(1, [1.0*angstroms, 2.0*angstroms, 3.0*angstroms])
self.assertEqual(force.getNumParticles(), 2)
self.assertEqual(force.getNumGlobalParameters(), 2)
self.assertEqual(force.getGlobalParameterName(0), 'k')
self.assertEqual(force.getGlobalParameterName(1), 'k2')
self.assertEqual(force.getGlobalParameterDefaultValue(0), 1000*4.184)
self.assertEqual(force.getGlobalParameterDefaultValue(1), 20)
i, (x0, y0, z0) = force.getParticleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(x0, 1)
self.assertEqual(y0, 2)
self.assertEqual(z0, 3)
i, (x0, y0, z0) = force.getParticleParameters(1)
self.assertEqual(i, 1)
self.assertAlmostEqual(x0, 1/10)
self.assertAlmostEqual(y0, 2/10)
self.assertAlmostEqual(z0, 3/10)
def testCustomGBForce(self):
""" Tests the CustomGBForce API features """
force = CustomGBForce()
force.addPerParticleParameter('q')
force.addPerParticleParameter('radius')
force.addPerParticleParameter('scale')
force.addGlobalParameter('extDiel', 78.5)
force.addGlobalParameter('intDiel', 1.0)
force.addComputedValue('I',
'step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*'
'(r-sr2^2/r)+0.5*log(L/U)/r+C);'
'U=r+sr2; C=2*(1/or1-1/L)*step(sr2-r-or1);'
'L=max(or1, D); D=abs(r-sr2); sr2=scale2*or2;'
'or1=radius1-0.009; or2=radius2-0.009',
CustomGBForce.ParticlePairNoExclusions
)
force.addComputedValue('B',
'1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);'
'psi=I*or; or=radius-0.009',
CustomGBForce.SingleParticle
)
force.addEnergyTerm('-138.935456*(1/intDiel-1/extDiel)*q1*q2/f;'
'f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))',
CustomGBForce.ParticlePair
)
force.setNonbondedMethod(CustomGBForce.CutoffPeriodic)
force.addParticle([1.0, 0.1, 0.5])
force.addParticle([-1.0*coulombs, 1.0*angstroms, 0.5])
self.assertEqual(force.getNumParticles(), 2)
self.assertEqual(force.getNumComputedValues(), 2)
self.assertEqual(force.getNumEnergyTerms(), 1)
self.assertEqual(force.getNumPerParticleParameters(), 3)
self.assertEqual(force.getPerParticleParameterName(0), 'q')
self.assertEqual(force.getPerParticleParameterName(1), 'radius')
self.assertEqual(force.getPerParticleParameterName(2), 'scale')
self.assertTrue(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomGBForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomGBForce.CutoffNonPeriodic)
self.assertFalse(force.usesPeriodicBoundaryConditions())
q, rad, scale = force.getParticleParameters(0)
self.assertEqual(q, 1.0)
self.assertEqual(rad, 0.1)
self.assertEqual(scale, 0.5)
q, rad, scale = force.getParticleParameters(1)
self.assertEqual(q, -6.24150962915265e+18) # very electronegative
self.assertEqual(rad, 0.1)
self.assertEqual(scale, 0.5)
force.setCutoffDistance(12*angstroms)
self.assertAlmostEqualUnit(force.getCutoffDistance(), 1.2*nanometers)
force.setCutoffDistance(1)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
def testCustomHBondForce(self):
""" Tests the CustomHbondForce API features """
force = CustomHbondForce('kd*(distance(a1,d1)-r0)^2 + '
'ka*(angle(a1,d1,d2)-theta0)^2')
force.addPerAcceptorParameter('r0')
force.addPerAcceptorParameter('ka')
force.addPerDonorParameter('theta0')
force.addPerDonorParameter('kd')
force.setCutoffDistance(10*angstroms)
self.assertEqual(force.getNumPerAcceptorParameters(), 2)
self.assertEqual(force.getNumPerDonorParameters(), 2)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
self.assertIs(force.getCutoffDistance().unit, nanometer)
force.addAcceptor(0, 1, 2, [0.2, 10.0])
force.addAcceptor(3, -1, -1, [4*angstroms,
20.0*kilocalories_per_mole/angstroms**2])
force.addDonor(4, 5, 6, [math.pi, 30])
force.addDonor(7, 8, -1, [180*degrees,
40*kilocalories_per_mole/radians**2])
self.assertEqual(force.getNumAcceptors(), 2)
self.assertEqual(force.getNumDonors(), 2)
i, j, k, (r0, ka) = force.getAcceptorParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(r0, 0.2)
self.assertEqual(ka, 10)
i, j, k, (r0, ka) = force.getAcceptorParameters(1)
self.assertEqual(i, 3)
self.assertEqual(j, -1)
self.assertEqual(k, -1)
self.assertEqual(r0, 0.4)
self.assertEqual(ka, 20*4.184*100)
i, j, k, (theta0, kd) = force.getDonorParameters(0)
self.assertEqual(i, 4)
self.assertEqual(j, 5)
self.assertEqual(k, 6)
self.assertEqual(theta0, math.pi)
self.assertEqual(kd, 30)
i, j, k, (theta0, kd) = force.getDonorParameters(1)
self.assertEqual(i, 7)
self.assertEqual(j, 8)
self.assertEqual(k, -1)
self.assertEqual(theta0, math.pi)
self.assertEqual(kd, 40*4.184)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomHbondForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomHbondForce.CutoffNonPeriodic)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomHbondForce.CutoffPeriodic)
self.assertTrue(force.usesPeriodicBoundaryConditions())
def testCustomNonbondedForce(self):
""" Tests the CustomNonbondedForce API features """
force = CustomNonbondedForce('4*diel*q1*q2/r+sqrt(p1*p2)/r^2-sqrt(m1*m2)/r^3')
force.addGlobalParameter('diel', 1.0)
force.addPerParticleParameter('q')
force.addPerParticleParameter('p')
force.addPerParticleParameter('m')
force.addParticle([1, 2, 3])
force.addParticle([1*coulombs, 2*kilocalories_per_mole*angstroms**2, 3*kilocalories_per_mole*angstroms**3])
self.assertEqual(force.getNumParticles(), 2)
charge, sigma, epsilon = force.getParticleParameters(0)
self.assertEqual(charge, 1)
self.assertEqual(sigma, 2)
self.assertEqual(epsilon, 3)
charge, sigma, epsilon = force.getParticleParameters(1)
self.assertEqual(charge, 6.24150962915265e+18) # very electronegative
self.assertEqual(sigma, 2*4.184/100)
self.assertAlmostEqual(epsilon, 3*4.184/1000)
force.setCutoffDistance(10*angstroms)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
force.setCutoffDistance(1)
self.assertEqual(force.getCutoffDistance(), 1*nanometers)
force.setSwitchingDistance(8*angstroms)
self.assertEqual(force.getSwitchingDistance(), 0.8*nanometers)
self.assertIs(force.getSwitchingDistance().unit, nanometer)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomNonbondedForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomNonbondedForce.CutoffNonPeriodic)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(CustomNonbondedForce.CutoffPeriodic)
self.assertTrue(force.usesPeriodicBoundaryConditions())
def testCustomManyParticleForce(self):
""" Tests the CustomManyParticleForce API features """
force = CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=k1*angle(p1,p2,p3); theta2=k2*angle(p2,p3,p1); theta3=k3*angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)")
force.setPermutationMode(CustomManyParticleForce.SinglePermutation)
force.setTypeFilter(0, [0])
force.setTypeFilter(1, [1])
force.setTypeFilter(2, [2])
force.addGlobalParameter('C', 1.0*kilocalories_per_mole)
force.addPerParticleParameter('k')
self.assertEqual(force.getNumGlobalParameters(), 1)
self.assertEqual(force.getGlobalParameterName(0), 'C')
self.assertEqual(force.getGlobalParameterDefaultValue(0), 4.184)
self.assertEqual(force.getNumPerParticleParameters(), 1)
force.addParticle([10], 0)
force.addParticle([20], 1)
force.addParticle([30*kilocalories_per_mole], 2)
self.assertEqual(force.getNumParticles(), 3)
self.assertEqual(force.getParticleParameters(0)[0][0], 10)
self.assertEqual(force.getParticleParameters(1)[0][0], 20)
self.assertEqual(force.getParticleParameters(2)[0][0], 30*4.184)
def testDrudeForce(self):
""" Tests the DrudeForce API features """
force = DrudeForce()
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.addParticle(0, 1, -1, -1, -1, 1, 1, 0, 0)
force.addParticle(1, 2, 3, -1, -1, 1*elementary_charge, 1*angstrom**3, 0.5, 0)
force.addParticle(2, 3, 4, 5, 6, 1*elementary_charge, 10*angstrom**3, 0.5, 0.5)
force.addScreenedPair(0, 1, 0.5)
force.addScreenedPair(1, 2, 0.25)
force.addScreenedPair(0, 2, 0.125)
self.assertEqual(force.getNumParticles(), 3)
self.assertEqual(force.getNumScreenedPairs(), 3)
i, j, k, l, m, q, a, an12, an34 = force.getParticleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, -1)
self.assertEqual(l, -1)
self.assertEqual(m, -1)
self.assertEqual(q, 1*elementary_charge)
self.assertEqual(a, 1*nanometer**3)
self.assertEqual(an12, 0)
self.assertEqual(an34, 0)
i, j, k, l, m, q, a, an12, an34 = force.getParticleParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, -1)
self.assertEqual(m, -1)
self.assertEqual(q, 1*elementary_charge)
self.assertAlmostEqualUnit(a, 1*angstrom**3)
self.assertEqual(an12, 0.5)
self.assertEqual(an34, 0)
i, j, k, l, m, q, a, an12, an34 = force.getParticleParameters(2)
self.assertEqual(i, 2)
self.assertEqual(j, 3)
self.assertEqual(k, 4)
self.assertEqual(l, 5)
self.assertEqual(m, 6)
self.assertEqual(q, 1*elementary_charge)
self.assertAlmostEqualUnit(a, 10*angstrom**3)
self.assertEqual(an12, 0.5)
self.assertEqual(an34, 0.5)
i, j, thole = force.getScreenedPairParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(thole, 0.5)
i, j, thole = force.getScreenedPairParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(thole, 0.25)
i, j, thole = force.getScreenedPairParameters(2)
self.assertEqual(i, 0)
self.assertEqual(j, 2)
self.assertEqual(thole, 0.125)
def testAmoebaBondForce(self):
""" Tests the AmoebaBondForce API features """
force1 = AmoebaBondForce()
force2 = AmoebaBondForce()
force1.setAmoebaGlobalBondCubic(1.5)
force2.setAmoebaGlobalBondCubic(1.5/angstrom)
force1.setAmoebaGlobalBondQuartic(1.5)
force2.setAmoebaGlobalBondQuartic(1.5/angstrom**2)
self.assertEqual(force1.getAmoebaGlobalBondCubic(), 1.5/nanometer)
self.assertEqual(force2.getAmoebaGlobalBondCubic(), 1.5/angstrom)
self.assertEqual(force1.getAmoebaGlobalBondQuartic(), 1.5/nanometer**2)
self.assertAlmostEqualUnit(force2.getAmoebaGlobalBondQuartic(), 1.5/angstrom**2)
force1.addBond(0, 1, 0.15, 10.0)
force1.addBond(1, 2, 1.5*angstroms, 10.0*kilocalories_per_mole/angstroms**2)
self.assertEqual(force1.getNumBonds(), 2)
self.assertEqual(force2.getNumBonds(), 0)
i, j, req, k = force1.getBondParameters(0)
self.assertEqual(req, 0.15*nanometers)
self.assertEqual(k, 10.0*kilojoules_per_mole/nanometers**2)
i, j, req, k = force1.getBondParameters(1)
self.assertAlmostEqualUnit(req, 1.5*angstroms)
self.assertAlmostEqualUnit(k, 10.0*kilocalories_per_mole/angstroms**2)
def testAmoebaAngleForce(self):
""" Tests the AmoebaAngleForce API features """
force = AmoebaAngleForce()
force.setAmoebaGlobalAngleCubic(1.0)
force.setAmoebaGlobalAngleQuartic(2.0/radians**2)
force.setAmoebaGlobalAnglePentic(3.0/degrees**3)
force.setAmoebaGlobalAngleSextic(4.0)
self.assertEqual(force.getAmoebaGlobalAngleCubic(), 1.0/radians)
self.assertEqual(force.getAmoebaGlobalAngleQuartic(), 2.0/radians**2)
self.assertAlmostEqualUnit(force.getAmoebaGlobalAnglePentic(), 3.0/degrees**3)
self.assertEqual(force.getAmoebaGlobalAngleSextic(), 4.0/radians**4)
force.addAngle(0, 1, 2, math.pi*radians, 1.5*kilocalories_per_mole/radians**2)
force.addAngle(1, 2, 3, 180*degrees, 1.5*kilocalories_per_mole/radians**2)
force.addAngle(2, 3, 4, 109.4, 1.5)
self.assertEqual(force.getNumAngles(), 3)
i, j, k, t, tk = force.getAngleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertAlmostEqualUnit(t, math.pi*radians)
self.assertIs(t.unit, degree)
self.assertAlmostEqualUnit(tk, 1.5*kilocalories_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
i, j, k, t, tk = force.getAngleParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertAlmostEqualUnit(t, 180*degrees)
self.assertIs(t.unit, degree)
self.assertAlmostEqualUnit(tk, 1.5*kilocalories_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
i, j, k, t, tk = force.getAngleParameters(2)
self.assertEqual(i, 2)
self.assertEqual(j, 3)
self.assertEqual(k, 4)
self.assertAlmostEqualUnit(t, 109.4*degrees)
self.assertIs(t.unit, degree)
self.assertAlmostEqualUnit(tk, 1.5*kilojoules_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
def testGeneralizedKirkwood(self):
""" Tests the AmoebaGeneralizedKirkwoodForce API features """
force = AmoebaGeneralizedKirkwoodForce()
self.assertEqual(force.getProbeRadius(), 0.14*nanometer) # default
force.setProbeRadius(0.16)
self.assertEqual(force.getProbeRadius(), 0.16*nanometer)
self.assertIs(force.getProbeRadius().unit, nanometer)
force.setProbeRadius(1.4*angstrom)
self.assertEqual(force.getProbeRadius(), 1.4*angstrom)
self.assertIs(force.getProbeRadius().unit, nanometer)
self.assertEqual(force.getSoluteDielectric(), 1.0) # default
force.setSoluteDielectric(2.0)
self.assertEqual(force.getSoluteDielectric(), 2.0)
self.assertEqual(force.getSolventDielectric(), 78.3) # default
force.setSolventDielectric(80)
self.assertEqual(force.getSolventDielectric(), 80)
self.assertEqual(force.getSurfaceAreaFactor(),
-170.35173066268223*kilojoule_per_mole/nanometer**2) # default
force.setSurfaceAreaFactor(-1.0*kilocalorie_per_mole/angstrom**2)
self.assertAlmostEqualUnit(force.getSurfaceAreaFactor(),
-1.0*kilocalorie_per_mole/angstrom**2) # default
force.addParticle(1.0*coulomb, 1.0*angstroms, 0.5)
force.addParticle(1.0, 1.0, 0.4)
self.assertEqual(force.getNumParticles(), 2)
q, r, s = force.getParticleParameters(0)
self.assertAlmostEqualUnit(q, 1.0*coulomb)
self.assertIs(q.unit, elementary_charge)
self.assertEqual(r, 1.0*angstroms)
self.assertIs(r.unit, nanometer)
self.assertEqual(s, 0.5)
q, r, s = force.getParticleParameters(1)
self.assertAlmostEqualUnit(q, 1.0*elementary_charge)
self.assertIs(q.unit, elementary_charge)
self.assertEqual(r, 1.0*nanometer)
self.assertIs(r.unit, nanometer)
self.assertEqual(s, 0.4)
def testAmoebaInPlaneAngleForce(self):
""" Tests the AmoebaInPlaneAngleForce API features """
force = AmoebaInPlaneAngleForce()
force.setAmoebaGlobalInPlaneAngleCubic(1.0)
self.assertEqual(force.getAmoebaGlobalInPlaneAngleCubic(), 1/radian)
self.assertEqual(str(force.getAmoebaGlobalInPlaneAngleCubic().unit), '/radian')
force.setAmoebaGlobalInPlaneAngleQuartic(1.0/degrees**2)
self.assertAlmostEqualUnit(force.getAmoebaGlobalInPlaneAngleQuartic(), 1/degrees**2)
self.assertEqual(str(force.getAmoebaGlobalInPlaneAngleQuartic().unit), '/(radian**2)')
force.setAmoebaGlobalInPlaneAnglePentic(1.0/radians**3)
self.assertEqual(force.getAmoebaGlobalInPlaneAnglePentic(), 1/radian**3)
self.assertEqual(str(force.getAmoebaGlobalInPlaneAnglePentic().unit), '/(radian**3)')
force.setAmoebaGlobalInPlaneAngleSextic(1.0/radians**4)
self.assertEqual(force.getAmoebaGlobalInPlaneAngleSextic(), 1/radian**4)
self.assertEqual(str(force.getAmoebaGlobalInPlaneAngleSextic().unit), '/(radian**4)')
force.addAngle(0, 1, 2, 3, math.pi, 1.0)
force.addAngle(1, 2, 3, 4, 180*degrees, 1.0*kilocalories_per_mole/radians**2)
self.assertEqual(force.getNumAngles(), 2)
i, j, k, l, t, tk = force.getAngleParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(t, math.pi*radians)
self.assertIs(t.unit, radians)
self.assertEqual(tk, 1.0*kilojoules_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
i, j, k, l, t, tk = force.getAngleParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertEqual(t, 180*degrees)
self.assertIs(t.unit, radians)
self.assertEqual(tk, 1.0*kilocalorie_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
def testAmoebaOutOfPlaneBendForce(self):
""" Tests the AmoebaOutOfPlaneBendForce API features """
force = AmoebaOutOfPlaneBendForce()
force.setAmoebaGlobalOutOfPlaneBendCubic(1.0)
self.assertEqual(force.getAmoebaGlobalOutOfPlaneBendCubic(), 1/radian)
self.assertEqual(str(force.getAmoebaGlobalOutOfPlaneBendCubic().unit), '/radian')
force.setAmoebaGlobalOutOfPlaneBendQuartic(1.0/degrees**2)
self.assertAlmostEqualUnit(force.getAmoebaGlobalOutOfPlaneBendQuartic(), 1/degrees**2)
self.assertEqual(str(force.getAmoebaGlobalOutOfPlaneBendQuartic().unit), '/(radian**2)')
force.setAmoebaGlobalOutOfPlaneBendPentic(1.0/radians**3)
self.assertEqual(force.getAmoebaGlobalOutOfPlaneBendPentic(), 1/radian**3)
self.assertEqual(str(force.getAmoebaGlobalOutOfPlaneBendPentic().unit), '/(radian**3)')
force.setAmoebaGlobalOutOfPlaneBendSextic(1.0/radians**4)
self.assertEqual(force.getAmoebaGlobalOutOfPlaneBendSextic(), 1/radian**4)
self.assertEqual(str(force.getAmoebaGlobalOutOfPlaneBendSextic().unit), '/(radian**4)')
force.addOutOfPlaneBend(0, 1, 2, 3, 1.0)
force.addOutOfPlaneBend(1, 2, 3, 4, 1.0*kilocalories_per_mole/radians**2)
self.assertEqual(force.getNumOutOfPlaneBends(), 2)
i, j, k, l, tk = force.getOutOfPlaneBendParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(tk, 1.0*kilojoules_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
i, j, k, l, tk = force.getOutOfPlaneBendParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertEqual(tk, 1.0*kilocalorie_per_mole/radians**2)
self.assertIs(tk.unit, kilojoules_per_mole/radians**2)
def testAmoebaPiTorsionForce(self):
""" Tests the AmoebaPiTorsionForce API features """
force = AmoebaPiTorsionForce()
force.addPiTorsion(0, 1, 2, 3, 4, 5, 1.0)
force.addPiTorsion(1, 2, 3, 4, 5, 6, 1.0*kilocalories_per_mole)
self.assertEqual(force.getNumPiTorsions(), 2)
i, j, k, l, m, n, tk = force.getPiTorsionParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(m, 4)
self.assertEqual(n, 5)
self.assertEqual(tk, 1.0*kilojoules_per_mole)
self.assertIs(tk.unit, kilojoule_per_mole)
i, j, k, l, m, n, tk = force.getPiTorsionParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertEqual(m, 5)
self.assertEqual(n, 6)
self.assertEqual(tk, 1.0*kilocalories_per_mole)
self.assertIs(tk.unit, kilojoule_per_mole)
def testAmoebaStretchBendForce(self):
""" Tests the AmoebaStretchBendForce API features """
force = AmoebaStretchBendForce()
force.addStretchBend(0, 1, 2, 0.10, 0.12, math.pi/2, 10.0, 12.0)
force.addStretchBend(1, 2, 3, 1.0*angstroms, 1.2*angstroms, 60*degrees,
10.0*kilocalories_per_mole/angstroms/radians,
12.0*kilocalories_per_mole/angstroms/radians)
self.assertEqual(force.getNumStretchBends(), 2)
i, j, k, r1, r2, t, k1, k2 = force.getStretchBendParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(r1, 0.1*nanometers)
self.assertIs(r1.unit, nanometers)
self.assertEqual(r2, 0.12*nanometers)
self.assertIs(r2.unit, nanometers)
self.assertEqual(t, math.pi/2*radians)
self.assertIs(t.unit, radians)
self.assertEqual(k1, 10*kilojoules_per_mole/nanometers/radians)
self.assertIs(k1.unit, kilojoules_per_mole/nanometers/radians)
self.assertEqual(k2, 12*kilojoules_per_mole/nanometers/radians)
self.assertIs(k2.unit, kilojoules_per_mole/nanometers/radians)
i, j, k, r1, r2, t, k1, k2 = force.getStretchBendParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(r1, 1.0*angstroms)
self.assertIs(r1.unit, nanometers)
self.assertEqual(r2, 1.2*angstroms)
self.assertIs(r2.unit, nanometers)
self.assertAlmostEqualUnit(t, 60*degrees)
self.assertIs(t.unit, radians)
self.assertEqual(k1, 10*kilocalories_per_mole/angstroms/radians)
self.assertIs(k1.unit, kilojoules_per_mole/nanometers/radians)
self.assertEqual(k2, 12*kilocalories_per_mole/angstroms/radians)
self.assertIs(k2.unit, kilojoules_per_mole/nanometers/radians)
def testAmoebaTorsionTorsionForce(self):
""" Tests the AmoebaTorsionTorsionForce API features """
force = AmoebaTorsionTorsionForce()
grid1 = [[[i, j, random.random(), random.random(), random.random(), random.random()]
for j in range(-180, 180, 24)] for i in range(-180, 180, 24)]
kcal = kilocalories_per_mole
grid2 = [[[i*math.pi/180*radians, j*math.pi/180*radians, random.random()*kcal,
random.random()*kcal/radians, random.random()*kcal/radians,
random.random()*kcal/radians**2]
for j in range(-180, 0, 10)] for i in range(-180, 0, 10)]
grid3 = [[[i, j, random.random()*kcal]
for j in range(-180, 180, 24)] for i in range(-180, 180, 24)]
force.setTorsionTorsionGrid(0, grid1)
force.setTorsionTorsionGrid(1, grid2)
force.setTorsionTorsionGrid(2, grid3)
self.assertEqual(force.getNumTorsionTorsionGrids(), 3)
# Check the grids
g1 = force.getTorsionTorsionGrid(0)
for row1, row2 in zip(g1, grid1):
for column1, column2 in zip(row1, row2):
self.assertEqual(len(column1), len(column2))
for x1, x2 in zip(column1, column2):
self.assertEqual(x1, x2)
g2 = force.getTorsionTorsionGrid(1)
for row1, row2 in zip(g2, grid2):
for column1, column2 in zip(row1, row2):
self.assertEqual(column1[0], column2[0].value_in_unit(degree))
self.assertEqual(column1[1], column2[1].value_in_unit(degree))
self.assertEqual(column1[2], column2[2].value_in_unit(kilojoules_per_mole))
self.assertEqual(column1[3], column2[3].value_in_unit(kilojoules_per_mole/radian))
self.assertEqual(column1[4], column2[4].value_in_unit(kilojoules_per_mole/radian))
self.assertEqual(column1[5], column2[5].value_in_unit(kilojoules_per_mole/radian**2))
g3 = force.getTorsionTorsionGrid(2)
for row1, row2 in zip(g3, grid3):
for column1, column2 in zip(row1, row2):
self.assertEqual(len(column1), 6)
self.assertEqual(len(column2), 3)
self.assertEqual(column1[0], column2[0])
self.assertEqual(column1[1], column2[1])
self.assertEqual(column1[2], column2[2].value_in_unit(kilojoules_per_mole))
force.addTorsionTorsion(0, 1, 2, 3, 4, 5, 0)
force.addTorsionTorsion(1, 2, 3, 4, 5, 6, 1)
force.addTorsionTorsion(2, 3, 4, 5, 6, 7, 2)
self.assertEqual(force.getNumTorsionTorsions(), 3)
i, j, k, l, m, ch, g = force.getTorsionTorsionParameters(0)
self.assertEqual(i, 0)
self.assertEqual(j, 1)
self.assertEqual(k, 2)
self.assertEqual(l, 3)
self.assertEqual(m, 4)
self.assertEqual(ch, 5)
self.assertEqual(g, 0)
i, j, k, l, m, ch, g = force.getTorsionTorsionParameters(1)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(l, 4)
self.assertEqual(m, 5)
self.assertEqual(ch, 6)
self.assertEqual(g, 1)
def testAmoebaVdwForce(self):
""" Tests the AmoebaVdwForce API features """
force = AmoebaVdwForce()
self.assertEqual(force.getSigmaCombiningRule(), 'CUBIC-MEAN')
force.setSigmaCombiningRule('ARITHMETIC')
self.assertEqual(force.getSigmaCombiningRule(), 'ARITHMETIC')
force.setSigmaCombiningRule('GEOMETRIC')
self.assertEqual(force.getSigmaCombiningRule(), 'GEOMETRIC')
self.assertEqual(force.getEpsilonCombiningRule(), 'HHG')
force.setEpsilonCombiningRule('HARMONIC')
self.assertEqual(force.getEpsilonCombiningRule(), 'HARMONIC')
force.setEpsilonCombiningRule('GEOMETRIC')
self.assertEqual(force.getEpsilonCombiningRule(), 'GEOMETRIC')
force.setEpsilonCombiningRule('ARITHMETIC')
self.assertEqual(force.getEpsilonCombiningRule(), 'ARITHMETIC')
self.assertTrue(force.getUseDispersionCorrection())
force.setUseDispersionCorrection(False)
self.assertFalse(force.getUseDispersionCorrection())
self.assertIs(force.getNonbondedMethod(), AmoebaVdwForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(AmoebaVdwForce.CutoffPeriodic)
self.assertTrue(force.usesPeriodicBoundaryConditions())
self.assertIs(force.getNonbondedMethod(), AmoebaVdwForce.CutoffPeriodic)
force.setCutoff(10.0*angstroms)
self.assertEqual(force.getCutoff(), 10.0*angstroms)
self.assertIs(force.getCutoff().unit, nanometers)
force.addParticle(0, 0.1, 1.0, 1.0)
force.addParticle(1, 1.0*angstroms, 1.0*kilocalories_per_mole, 0.5)
force.addParticle(1, 0.8*angstroms, 2.0*kilocalories_per_mole, 0.25)
self.assertEqual(force.getNumParticles(), 3)
p, sig, eps, scale = force.getParticleParameters(0)
self.assertEqual(p, 0)
self.assertEqual(sig, 0.1*nanometers)
self.assertIs(sig.unit, nanometers)
self.assertEqual(eps, 1.0*kilojoules_per_mole)
self.assertIs(eps.unit, kilojoules_per_mole)
self.assertEqual(scale, 1.0)
p, sig, eps, scale = force.getParticleParameters(1)
self.assertEqual(p, 1)
self.assertEqual(sig, 1.0*angstroms)
self.assertIs(sig.unit, nanometers)
self.assertEqual(eps, 1.0*kilocalories_per_mole)
self.assertIs(eps.unit, kilojoules_per_mole)
self.assertEqual(scale, 0.5)
p, sig, eps, scale = force.getParticleParameters(2)
self.assertEqual(p, 1)
self.assertAlmostEqualUnit(sig, 0.8*angstroms)
self.assertIs(sig.unit, nanometers)
self.assertEqual(eps, 2.0*kilocalories_per_mole)
self.assertIs(eps.unit, kilojoules_per_mole)
self.assertEqual(scale, 0.25)
def testAmoebaWcaDispersionForce(self):
""" Tests the AmoebaWcaDispersionForce API features """
force = AmoebaWcaDispersionForce()
self.assertEqual(force.getDispoff(), 0.26*nanometer)
self.assertEqual(force.getAwater(), 0.033428*nanometer**-3)
self.assertEqual(force.getEpsh(), 0.0135*kilojoule_per_mole)
self.assertEqual(force.getEpso(), 0.11*kilojoule_per_mole)
self.assertEqual(force.getRminh(), 1.3275*nanometer)
self.assertEqual(force.getRmino(), 1.7025*nanometer)
self.assertEqual(force.getShctd(), 0.81)
self.assertEqual(force.getSlevy(), 1.0)
force.setDispoff(3*angstroms)
self.assertAlmostEqualUnit(force.getDispoff(), 3*angstroms)
self.assertIs(force.getDispoff().unit, nanometer)
force.setAwater(3*angstroms**-3)
self.assertAlmostEqualUnit(force.getAwater(), 3*angstroms**-3)
self.assertEqual(1*force.getAwater().unit, 1*nanometer**-3)
force.setEpsh(1*kilocalorie_per_mole)
self.assertEqual(force.getEpsh(), 1*kilocalorie_per_mole)
self.assertIs(force.getEpsh().unit, kilojoule_per_mole)
force.setEpso(1*kilocalorie_per_mole)
self.assertEqual(force.getEpso(), 1*kilocalorie_per_mole)
self.assertIs(force.getEpso().unit, kilojoule_per_mole)
force.setRminh(20*angstroms)
self.assertEqual(force.getRminh(), 20*angstroms)
self.assertIs(force.getRminh().unit, nanometer)
force.setRmino(30*angstroms)
self.assertEqual(force.getRmino(), 30*angstroms)
self.assertIs(force.getRmino().unit, nanometer)
force.setShctd(1)
self.assertEqual(force.getShctd(), 1)
force.setSlevy(2)
self.assertEqual(force.getSlevy(), 2)
force.addParticle(0.5, 1)
force.addParticle(3*angstroms, 1*kilocalorie_per_mole)
self.assertEqual(force.getNumParticles(), 2)
sig, eps = force.getParticleParameters(0)
self.assertEqual(sig, 0.5*nanometer)
self.assertIs(sig.unit, nanometer)
self.assertEqual(eps, 1*kilojoule_per_mole)
self.assertIs(eps.unit, kilojoule_per_mole)
sig, eps = force.getParticleParameters(1)
self.assertAlmostEqualUnit(sig, 3*angstrom)
self.assertIs(sig.unit, nanometer)
self.assertEqual(eps, 1*kilocalorie_per_mole)
self.assertIs(eps.unit, kilojoule_per_mole)
def testAmoebaMultipoleForce(self):
""" Tests the AmoebaMultipoleForce API features """
force = AmoebaMultipoleForce()
self.assertIs(force.getNonbondedMethod(), AmoebaMultipoleForce.NoCutoff)
self.assertFalse(force.usesPeriodicBoundaryConditions())
force.setNonbondedMethod(AmoebaMultipoleForce.PME)
self.assertIs(force.getNonbondedMethod(), AmoebaMultipoleForce.PME)
self.assertTrue(force.usesPeriodicBoundaryConditions())
self.assertEqual(force.getCutoffDistance(), 1*nanometer)
self.assertIs(force.getCutoffDistance().unit, nanometer)
force.setCutoffDistance(8*angstroms)
self.assertEqual(force.getCutoffDistance(), 8*angstrom)
self.assertIs(force.getCutoffDistance().unit, nanometer)
self.assertEqual(force.getPolarizationType(), AmoebaMultipoleForce.Mutual)
force.setPolarizationType(AmoebaMultipoleForce.Direct)
self.assertEqual(force.getPolarizationType(), AmoebaMultipoleForce.Direct)
force.setPolarizationType(AmoebaMultipoleForce.Mutual)
self.assertEqual(force.getPolarizationType(), AmoebaMultipoleForce.Mutual)
force.addMultipole(1.0, [0.5, 0, -0.5], list(range(9)),
AmoebaMultipoleForce.ZThenX, 1, 2, 3, 0.5, 0.5, 1.0)
force.addMultipole(1.0*elementary_charge, [0.5, 0, -0.5]*elementary_charge/angstrom,
list(range(9))*elementary_charge/angstrom**2,
AmoebaMultipoleForce.Bisector, 2, 3, 4, 0.5, 0.5, 1.0*angstrom**3)
self.assertEqual(force.getNumMultipoles(), 2)
q, mu, quad, ax, i, j, k, thole, damp, polarity = force.getMultipoleParameters(0)
self.assertEqual(q, 1.0*elementary_charge)
self.assertEqual(mu, (0.5, 0, -0.5)*elementary_charge/nanometer)
self.assertEqual(quad, tuple(range(9))*elementary_charge/nanometer**2)
self.assertEqual(ax, AmoebaMultipoleForce.ZThenX)
self.assertEqual(i, 1)
self.assertEqual(j, 2)
self.assertEqual(k, 3)
self.assertEqual(thole, 0.5)
self.assertEqual(damp, 0.5)
self.assertEqual(polarity, 1*nanometer**3)
q, mu, quad, ax, i, j, k, thole, damp, polarity = force.getMultipoleParameters(1)
self.assertEqual(q, 1.0*elementary_charge)
self.assertEqual(mu, (0.5, 0, -0.5)*elementary_charge/angstrom)
self.assertAlmostEqualUnitArray(quad, tuple(range(9))*elementary_charge/angstrom**2)
self.assertEqual(ax, AmoebaMultipoleForce.Bisector)
self.assertEqual(i, 2)
self.assertEqual(j, 3)
self.assertEqual(k, 4)
self.assertEqual(thole, 0.5)
self.assertEqual(damp, 0.5)
self.assertAlmostEqualUnit(polarity, 1*angstrom**3)
def testVerletIntegrator(self):
""" Tests the VerletIntegrator API features """
integrator = VerletIntegrator(1.0)
self.assertEqual(integrator.getStepSize(), 1.0*picosecond)
self.assertEqual(integrator.getConstraintTolerance(), 1e-5)
integrator.setConstraintTolerance(1e-6)
self.assertEqual(integrator.getConstraintTolerance(), 1e-6)
integrator = VerletIntegrator(1.0*femtoseconds)
self.assertEqual(integrator.getStepSize(), 1.0*femtoseconds)
def testVariableVerletIntegrator(self):
""" Tests the VariableVerletIntegrator API features """
integrator = VariableVerletIntegrator(0.1)
self.assertEqual(integrator.getErrorTolerance(), 0.1)
integrator.setErrorTolerance(0.01)
self.assertEqual(integrator.getErrorTolerance(), 0.01)
self.assertEqual(integrator.getConstraintTolerance(), 1e-5)
integrator.setConstraintTolerance(1e-6)
self.assertEqual(integrator.getConstraintTolerance(), 1e-6)
def testLangevinIntegrator(self):
""" Tests the LangevinIntegrator API features """
integrator = LangevinIntegrator(300, 0.1, 1)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertEqual(integrator.getFriction(), 0.1/picosecond)
self.assertEqual(integrator.getStepSize(), 1*picosecond)
integrator = LangevinIntegrator(300*kelvin, 0.1/microsecond, 1*femtosecond)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertAlmostEqualUnit(integrator.getFriction(), 0.1/microsecond)
self.assertEqual(integrator.getStepSize(), 1*femtosecond)
def testVariableLangevinIntegrator(self):
""" Tests the VariableLangevinIntegrator API features """
integrator = VariableLangevinIntegrator(300, 0.1, 0.1)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertEqual(integrator.getFriction(), 0.1/picosecond)
self.assertEqual(integrator.getErrorTolerance(), 0.1)
integrator = VariableLangevinIntegrator(300*kelvin, 0.1/microsecond, 0.01)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertAlmostEqualUnit(integrator.getFriction(), 0.1/microsecond)
self.assertEqual(integrator.getErrorTolerance(), 0.01)
def testBrownianIntegrator(self):
""" Tests the BrownianIntegrator API features """
integrator = BrownianIntegrator(300, 0.1, 1)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertEqual(integrator.getFriction(), 0.1/picosecond)
self.assertEqual(integrator.getStepSize(), 1*picosecond)
integrator = BrownianIntegrator(300*kelvin, 0.1/microsecond, 1*femtosecond)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
self.assertAlmostEqualUnit(integrator.getFriction(), 0.1/microsecond)
self.assertEqual(integrator.getStepSize(), 1*femtosecond)
def testAndersenThermostat(self):
""" Tests the AndersenThermostat API features """
force = AndersenThermostat(300*kelvin, 1/microsecond)
self.assertEqual(force.getDefaultTemperature(), 300*kelvin)
self.assertAlmostEqualUnit(force.getDefaultCollisionFrequency(), 1/microsecond)
force.setDefaultTemperature(298.15)
force.setDefaultCollisionFrequency(1)
self.assertEqual(force.getDefaultTemperature(), 298.15*kelvin)
self.assertAlmostEqualUnit(force.getDefaultCollisionFrequency(), 1/picosecond)
def testDrudeSCFIntegrator(self):
""" Tests the DrudeSCFIntegrator API features """
integrator = DrudeSCFIntegrator(0.002)
self.assertEqual(integrator.getStepSize(), 0.002*picoseconds)
self.assertAlmostEqualUnit(integrator.getMinimizationErrorTolerance(),
0.1*kilojoule_per_mole/nanometer)
integrator.setMinimizationErrorTolerance(1*kilocalorie_per_mole/angstrom)
self.assertAlmostEqualUnit(integrator.getMinimizationErrorTolerance(),
1*kilocalorie_per_mole/angstrom)
def testDrudeLangevinIntegrator(self):
""" Tests the DrudeLangevinIntegrator API features """
integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/microsecond,
100*kelvin, 1/picosecond, 0.1*femtosecond)
self.assertEqual(integrator.getTemperature(), 300*kelvin)
integrator.setTemperature(298.15)
self.assertEqual(integrator.getTemperature(), 298.15*kelvin)
self.assertAlmostEqualUnit(integrator.getFriction(), 1/microsecond)
integrator.setFriction(1)
self.assertEqual(integrator.getFriction(), 1/picosecond)
self.assertEqual(integrator.getDrudeTemperature(), 100*kelvin)
integrator.setDrudeTemperature(50)
self.assertEqual(integrator.getDrudeTemperature(), 50*kelvin)
self.assertEqual(integrator.getStepSize(), 0.1*femtosecond)
integrator.setStepSize(0.0005)
self.assertEqual(integrator.getStepSize(), 0.0005*picosecond)
def testCustomIntegrator(self):
""" Tests the CustomIntegrator API features """
integrator = CustomIntegrator(1.0)
self.assertEqual(integrator.getStepSize(), 1.0*picosecond)
self.assertEqual(integrator.getConstraintTolerance(), 1e-5)
integrator.setConstraintTolerance(1e-6)
self.assertEqual(integrator.getConstraintTolerance(), 1e-6)
integrator = CustomIntegrator(1.0*femtoseconds)
self.assertEqual(integrator.getStepSize(), 1.0*femtoseconds)
if __name__ == '__main__':
unittest.main()
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment