testInstallation.py

from __future__ import print_function
from functools import wraps
import os
import sys
# First make sure OpenMM is installed.

class TestingError(Exception):
    """
    An error is encountered when 
    """
    pass

try:
    from simtk.openmm.app import *
    from simtk.openmm import *
    from simtk.unit import *
except ImportError as err:
    simtk_import_failed = True
    simtk_import_error = err.message
else:
    simtk_import_failed = False

def error_converter(error_type):
    """ Converts all exceptions to the given Exception type """
    def wrapper(func):
        @wraps(func)
        def new_func(*args, **kwargs):
            try:
                func(*args, **kwargs)
            except error_type:
                # Pass the existing error through
                raise
            except BaseException as err:
                raise TestingError('Problem with OpenMM installation '
                        'encountered. OpenMM will not work until the problem '
                        'has been fixed.\n\nError message: %s' % err.message)
        return new_func
    return wrapper

@error_converter(TestingError)
def run_tests():
    """
    Runs a set of tests to determine which platforms are available and tests the
    relative accuracy between them. This can be used to determine if the Python
    API is installed and working properly, as well as the fidelity of the
    underlying OpenMM libraries with respect to computing energies and forces on
    the different platforms supported by your installation.

    This test prints the available platforms and the relative force errors
    between them for a test system. If a problem is detected, TestingError is
    raised.
    """
    if simtk_import_failed:
        raise TestingError('Failed to import OpenMM packages; OpenMM will not work.\n'
                           'Make sure OpenMM is installed and the library path is set correctly.'
                           '\n\nError message: %s' % simtk_import_error)
    # Create a System for the tests.
    data_dir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), 'openmm', 'app', 'data')
    pdb = PDBFile(os.path.join(data_dir, 'test.pdb'))
    forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
    system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
    
    # List all installed platforms and compute forces with each one.
    
    numPlatforms = Platform.getNumPlatforms()
    print("There are", numPlatforms, "Platforms available:")
    print()
    forces = [None]*numPlatforms
    platformErrors = {}
    for i in range(numPlatforms):
        platform = Platform.getPlatform(i)
        print(i+1, platform.getName(), end=" ")
        integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
        try:
            simulation = Simulation(pdb.topology, system, integrator, platform)
            simulation.context.setPositions(pdb.positions)
            forces[i] = simulation.context.getState(getForces=True).getForces()
            del simulation
            print("- Successfully computed forces")
        except:
            print("- Error computing forces with", platform.getName(), "platform")
            platformErrors[platform.getName()] = sys.exc_info()[1]
    
    # Give details of any errors.
    
    for platform in platformErrors:
        print()
        print("%s platform error: %s" % (platform, platformErrors[platform]))
    
    # See how well the platforms agree.
    
    if numPlatforms > 1:
        print()
        print("Median difference in forces between platforms:")
        print()
        for i in range(numPlatforms):
            for j in range(i):
                if forces[i] is not None and forces[j] is not None:
                    errors = []
                    for f1, f2 in zip(forces[i], forces[j]):
                        d = f1-f2
                        error = sqrt((d[0]*d[0]+d[1]*d[1]+d[2]*d[2])/(f1[0]*f1[0]+f1[1]*f1[1]+f1[2]*f1[2]))
                        errors.append(error)
                    print("{} vs. {}: {:g}".format(Platform.getPlatform(j).getName(),
                                                  Platform.getPlatform(i).getName(),
                                                  sorted(errors)[len(errors)//2]))

if __name__ == '__main__':

    try:
        run_tests()
    except TestingError as err:
        print(err.message)
        sys.exit(1)