mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
3645e1eeb7
* Variable displacements based on particle positions
* set variable displacements when adding particles
* update documentation
* address compilation error in OpenMMFortranWrapper
* update python API tests
* fix stray 'and'
* addParticle() without arguments add a particle that is not displaced
* pack displacement particles into int4
* put back default displacement removed in error
* ATMForce interface with coordinate transformation objects
* revise variable displacement API
* documentation, formatting, serialization
* Fixed C and Fortran wrappers
* Fixed Python wrappers
* Fixed factory
* Sort files to ensure classes are listed in the correct order
* Converted APIUnits test to new ATMForce API
* write class name
* skip the documentation for forward declarations
* undo 9e91d0b since it does not fix the doc build
* remove temporary doc files for nested classes
* Clean away tabs
---------
Co-authored-by: Peter Eastman <peastman@stanford.edu>
103 lines
3.5 KiB
Python
103 lines
3.5 KiB
Python
import unittest
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from openmm import *
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from openmm.app import *
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from openmm.unit import *
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class TestATMForce(unittest.TestCase):
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"""Tests the ATMForce"""
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def test2ParticlesNonbonded(self):
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"""Test for a Nonbonded force previously added to the System"""
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system = System()
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system.addParticle(1.0)
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system.addParticle(1.0)
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nbforce = NonbondedForce();
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nbforce.addParticle( 1.0, 1.0, 1.0)
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nbforce.addParticle(-1.0, 1.0, 1.0)
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system.addForce(nbforce)
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atmforce = ATMForce(0.5, 0.5, 0, 0, 0, 0, 0, 0, 1.0)
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atmforce.addParticle()
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p = atmforce.addParticle()
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atmforce.setParticleTransformation(p, FixedDisplacement(Vec3(1., 0., 0.)))
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atmforce.addForce(copy.copy(nbforce))
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system.removeForce(0)
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system.addForce(atmforce)
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integrator = VerletIntegrator(1.0)
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platform = Platform.getPlatform('Reference')
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context = Context(system, integrator, platform)
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positions = []
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positions.append(Vec3(0., 0., 0.))
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positions.append(Vec3(1., 0., 0.))
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context.setPositions(positions)
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state = context.getState(getEnergy = True, getForces = True)
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epot = state.getPotentialEnergy()
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(u1, u0, energy) = atmforce.getPerturbationEnergy(context)
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epert = u1 - u0
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#print("Potential energy = ", epot)
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#print("ATM perturbation energy = ", epert)
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epot_expected = -104.2320*kilojoules_per_mole
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epert_expected = 69.4062*kilojoules_per_mole
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assert( abs(epot-epot_expected) < 1.e-3*kilojoules_per_mole )
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assert( abs(epert-epert_expected) < 1.e-3*kilojoules_per_mole )
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assert isinstance(atmforce.getParticleTransformation(0), FixedDisplacement)
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def test3ParticlesNonbondedSwap(self):
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"""Test coordinate swap"""
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system = System()
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system.addParticle(1.0)
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system.addParticle(1.0)
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system.addParticle(1.0)
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nbforce = NonbondedForce();
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nbforce.addParticle( 0.0, 1.0, 1.0)
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nbforce.addParticle( 1.0, 1.0, 1.0)
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nbforce.addParticle(-1.0, 1.0, 1.0)
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atmforce = ATMForce(0.5, 0.5, 0, 0, 0, 0, 0, 0, 1.0)
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atmforce.addParticle() #particle 0 is not displaced
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#particle 1's coordinate is swapped with 2
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p = atmforce.addParticle()
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atmforce.setParticleTransformation(p, ParticleOffsetDisplacement(2, 1))
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#particle 2's coordinate is swapped with 1
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p = atmforce.addParticle()
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atmforce.setParticleTransformation(p, ParticleOffsetDisplacement(1, 2))
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atmforce.addForce(nbforce)
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system.addForce(atmforce)
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integrator = VerletIntegrator(1.0)
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platform = Platform.getPlatform('Reference')
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context = Context(system, integrator, platform)
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positions = []
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positions.append(Vec3( 0., 0., 0.))
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positions.append(Vec3( 1., 0., 0.))
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positions.append(Vec3(-1., 0., 0.))
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context.setPositions(positions)
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state = context.getState(getEnergy = True, getForces = True)
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epot = state.getPotentialEnergy()
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(u1, u0, energy) = atmforce.getPerturbationEnergy(context)
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epert = u1 - u0
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#print("Potential energy = ", epot)
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#print("ATM perturbation energy = ", epert)
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epot_expected = -69.52925*kilojoules_per_mole
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epert_expected = 0*kilojoules_per_mole
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assert( abs(epot-epot_expected) < 1.e-3*kilojoules_per_mole )
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assert( abs(epert-epert_expected) < 1.e-3*kilojoules_per_mole )
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