예제 #1
0
파일: _quench.py 프로젝트: wwwtyro/PyGMIN
def fire(coords, getEnergyGradient, tol = 1e-3, nsteps=100000, maxstep = 0.5, **kwargs):
    """
    A wrapper function for the pygmin FIRE implementation
    """
    opt = Fire(coords, getEnergyGradient, maxmove = maxstep, **kwargs)
    opt.run(fmax=tol, steps=nsteps)
    e,g = getEnergyGradient(opt.coords)
    rms = np.linalg.norm(g)/np.sqrt(len(g))
    return opt.coords, e, rms, opt.nsteps
예제 #2
0
def fire(coords, pot, tol=1e-3, nsteps=100000, **kwargs):
    """
    A wrapper function for the pygmin FIRE implementation
    """
    if not hasattr(pot, "getEnergyGradient"):
        # for compatibility with old quenchers.
        # assume pot is a getEnergyGradient function
        pot = _getEnergyGradientWrapper(pot)
    opt = Fire(coords, pot, **kwargs)
    res = opt.run(fmax=tol, steps=nsteps)
    return res
예제 #3
0
파일: _quench.py 프로젝트: js850/PyGMIN
def fire(coords, pot, tol=1e-3, nsteps=100000, **kwargs):
    """
    A wrapper function for the pygmin FIRE implementation
    """
    if not hasattr(pot, "getEnergyGradient"):
        # for compatibility with old quenchers.
        # assume pot is a getEnergyGradient function
        pot = _getEnergyGradientWrapper(pot)
    opt = Fire(coords, pot, **kwargs)
    res = opt.run(fmax=tol, steps=nsteps)
    return res
예제 #4
0
def fire(coords, getEnergyGradient, tol=1e-3, nsteps=100000, **kwargs):
    """
    A wrapper function for the pygmin FIRE implementation
    """
    if hasattr(getEnergyGradient, "getEnergyGradient"):
        # this is to aid compatibility between old and new quenchers.
        # This function will now accept a potential object
        getEnergyGradient = getEnergyGradient.getEnergyGradient
    pot = getEnergyGradientWrapper(getEnergyGradient)
    opt = Fire(coords, pot, **kwargs)
    opt.run(fmax=tol, steps=nsteps)
    e, g = getEnergyGradient(opt.coords)
    rms = np.linalg.norm(g) / np.sqrt(len(g))
    return opt.coords, e, rms, opt.nsteps
예제 #5
0
def fire(coords, getEnergyGradient, tol=1e-3, nsteps=100000, **kwargs):
    """
    A wrapper function for the pygmin FIRE implementation
    """
    if hasattr(getEnergyGradient, "getEnergyGradient"):
        # this is to aid compatibility between old and new quenchers.
        # This function will now accept a potential object
        getEnergyGradient = getEnergyGradient.getEnergyGradient
    pot = getEnergyGradientWrapper(getEnergyGradient)
    opt = Fire(coords, pot, **kwargs)
    opt.run(fmax=tol, steps=nsteps)
    e,g = getEnergyGradient(opt.coords)
    rms = np.linalg.norm(g)/np.sqrt(len(g))
    return opt.coords, e, rms, opt.nsteps