def __init__(self,
topology,
pathtoplumed="",
timestep=1.,
kbt=1.,
molinfo="",
logfile="plumed.log"):
"""
Parameters
----------
topology : :obj:`openpathsampling.engines.openmm.MDTopology`
pathtoplumed : string
path to the PLUMED installation
timestep : double
Time step size of the simulation in PLUMED default units (ps).
kbt : double
:math:`$k_BT$` in PLUMED default units (kJ/mol).
molinfo : string
A PDB file containing information about the molecule. (see
https://plumed.github.io/doc-v2.4/user-doc/html/_m_o_l_i_n_f_o.html).
logfile : string
Name of the PLUMED log file.
"""
self.interface = plumed.Plumed() # 8 is default size of real
self.pathtoplumed = pathtoplumed
self.topology = topology
self.timestep = timestep
self.kbt = kbt
self.molinfo = molinfo
self.logfile = logfile
self._commandlist = []
self._init_plumed()
def __init__(
self,
latency=1.0e-3,
name="",
pars=None,
dopbc=False,
threaded=False,
init_file="",
plumeddat="",
plumedstep=0,
):
"""Initialises FFPlumed.
Args:
pars: Optional dictionary, giving the parameters needed by the driver.
"""
# a socket to the communication library is created or linked
if plumed is None:
raise ImportError(
"Cannot find plumed libraries to link to a FFPlumed object/")
super(FFPlumed, self).__init__(latency,
name,
pars,
dopbc=False,
threaded=threaded)
self.plumed = plumed.Plumed()
self.plumeddat = plumeddat
self.plumedstep = plumedstep
self.init_file = init_file
if self.init_file.mode == "xyz":
infile = open(self.init_file.value, "r")
myframe = read_file(self.init_file.mode, infile)
myatoms = myframe["atoms"]
mycell = myframe["cell"]
myatoms.q *= unit_to_internal("length", self.init_file.units, 1.0)
mycell.h *= unit_to_internal("length", self.init_file.units, 1.0)
self.natoms = myatoms.natoms
self.plumed.cmd("setNatoms", self.natoms)
self.plumed.cmd("setPlumedDat", self.plumeddat)
self.plumed.cmd("setTimestep", 1.0)
self.plumed.cmd(
"setMDEnergyUnits", 2625.4996
) # Pass a pointer to the conversion factor between the energy unit used in your code and kJ mol-1
self.plumed.cmd(
"setMDLengthUnits", 0.052917721
) # Pass a pointer to the conversion factor between the length unit used in your code and nm
self.plumed.cmd("setMDTimeUnits", 2.4188843e-05)
self.plumedrestart = False
if self.plumedstep > 0:
# we are restarting, signal that PLUMED should continue
self.plumedrestart = True
self.plumed.cmd("setRestart", 1)
self.plumed.cmd("init")
self.charges = dstrip(myatoms.q) * 0.0
self.masses = dstrip(myatoms.m)
self.lastq = np.zeros(3 * self.natoms)
def test(self):
comm = MPI.COMM_WORLD
p = plumed.Plumed()
p.cmd("setNatoms", 2)
p.cmd("setLogFile", "test.log")
p.cmd("setMPIComm", comm)
p.cmd("init")
def test():
p = plumed.Plumed()
p.cmd("setNatoms", 2)
p.cmd("setLogFile", "test.log")
p.cmd("init")
p.cmd("readInputLine", "d: DISTANCE ATOMS=1,2")
p.cmd("readInputLine", "RESTRAINT ARG=d AT=0 KAPPA=1")
box = array.array('d', [10, 0, 0, 0, 10, 0, 0, 0, 10])
virial = array.array('d', [0, 0, 0, 0, 0, 0, 0, 0, 0])
masses = array.array('d', [1, 1])
charges = array.array('d', [0, 0])
forces = array.array('d', [0, 0, 0, 0, 0, 0])
positions = array.array('d', [0, 0, 0, 1, 2, 3])
p.cmd("setStep", 0)
p.cmd("setBox", box)
p.cmd("setMasses", masses)
p.cmd("setCharges", charges)
p.cmd("setPositions", positions)
p.cmd("setForces", forces)
p.cmd("setVirial", virial)
p.cmd("calc")
bias = array.array('d', [0])
p.cmd("getBias", bias)
assert (bias[0] - 7.0)**2 < 1e-8
assert (forces[0] - 1.0)**2 < 1e-8
assert (forces[1] - 2.0)**2 < 1e-8
assert (forces[2] - 3.0)**2 < 1e-8
assert (forces[3] + 1.0)**2 < 1e-8
assert (forces[4] + 2.0)**2 < 1e-8
assert (forces[5] + 3.0)**2 < 1e-8
def test(self):
p = plumed.Plumed()
p.cmd("setNatoms", 2)
p.cmd("setLogFile", "test.log")
p.cmd("init")
p.cmd("readInputLine", "d: DISTANCE ATOMS=1,2")
p.cmd("readInputLine", "RESTRAINT ARG=d AT=0 KAPPA=1")
box = array.array('d', [10, 0, 0, 0, 10, 0, 0, 0, 10])
virial = array.array('d', [0, 0, 0, 0, 0, 0, 0, 0, 0])
masses = array.array('d', [1, 1])
charges = array.array('d', [0, 0])
forces = array.array('d', [0, 0, 0, 0, 0, 0])
positions = array.array('d', [0, 0, 0, 1, 2, 3])
p.cmd("setStep", 0)
p.cmd("setBox", box)
p.cmd("setMasses", masses)
p.cmd("setCharges", charges)
p.cmd("setPositions", positions)
p.cmd("setForces", forces)
p.cmd("setVirial", virial)
p.cmd("calc")
bias = array.array('d', [0])
p.cmd("getBias", bias)
self.assertAlmostEqual(bias[0], 7.0)
self.assertAlmostEqual(forces[0], 1.0)
self.assertAlmostEqual(forces[1], 2.0)
self.assertAlmostEqual(forces[2], 3.0)
self.assertAlmostEqual(forces[3], -1.0)
self.assertAlmostEqual(forces[4], -2.0)
self.assertAlmostEqual(forces[5], -3.0)
# Output to four decimal places only
np.set_printoptions(precision=4)
# Read trajectory
traj = read_xyz("traj.xyz")
num_frames = len(traj)
num_atoms = traj[0].shape[0]
# Create arrays for stuff
box = np.diag(12.41642 * np.ones(3, dtype=np.float64))
virial = np.zeros((3, 3), dtype=np.float64)
masses = np.ones(num_atoms, dtype=np.float64)
forces = np.random.rand(num_atoms, 3)
charges = np.zeros(num_atoms, dtype=np.float64)
# Create PLUMED object and read input
p = plumed.Plumed()
p.cmd("setMDEngine", "python")
p.cmd("setTimestep", 1.)
p.cmd("setKbT", 1.)
p.cmd("setNatoms", num_atoms)
p.cmd("setLogFile", "test.log")
p.cmd("init")
p.cmd("readInputLine", "MOLINFO STRUCTURE=template.pdb")
t1 = create_plumed_var(p, "t1", "TORSION ATOMS=@phi-2")
t2 = create_plumed_var(p, "t2", "TORSION ATOMS=@psi-2")
t3 = create_plumed_var(p, "t3", "TORSION ATOMS=@phi-3")
t4 = create_plumed_var(p, "t4", "TORSION ATOMS=@psi-3")
t5 = create_plumed_var(p, "t5", "TORSION ATOMS=@phi-4")
t6 = create_plumed_var(p, "t6", "TORSION ATOMS=@psi-4")
t7 = create_plumed_var(p, "t7", "TORSION ATOMS=@phi-5")
t8 = create_plumed_var(p, "t8", "TORSION ATOMS=@psi-5")
def test():
os.chdir('test/')
os.system('rm -f bck.*')
# Output to four decimal places only
np.set_printoptions(precision=4)
# Read trajectory
traj = read_xyz("traj.xyz")
num_frames = len(traj)
num_atoms = traj[0].shape[0]
# Create arrays for stuff
box=np.diag(12.41642*np.ones(3,dtype=np.float64))
virial=np.zeros((3,3),dtype=np.float64)
masses=np.ones(num_atoms,dtype=np.float64)
forces=np.random.rand(num_atoms,3)
charges=np.zeros(num_atoms,dtype=np.float64)
# Create PLUMED object and read input
p = plumed.Plumed()
p.cmd("setMDEngine","python")
p.cmd("setTimestep", 1.)
p.cmd("setKbT", 1.)
p.cmd("setNatoms",num_atoms)
p.cmd("setLogFile","test.log")
p.cmd("init")
p.cmd("readInputLine","MOLINFO STRUCTURE=template.pdb")
t1 = create_plumed_var( p, "t1", "TORSION ATOMS=@phi-2" )
t2 = create_plumed_var( p, "t2", "TORSION ATOMS=@psi-2" )
t3 = create_plumed_var( p, "t3", "TORSION ATOMS=@phi-3" )
t4 = create_plumed_var( p, "t4", "TORSION ATOMS=@psi-3" )
t5 = create_plumed_var( p, "t5", "TORSION ATOMS=@phi-4" )
t6 = create_plumed_var( p, "t6", "TORSION ATOMS=@psi-4" )
t7 = create_plumed_var( p, "t7", "TORSION ATOMS=@phi-5" )
t8 = create_plumed_var( p, "t8", "TORSION ATOMS=@psi-5" )
t9 = create_plumed_var( p, "t9", "TORSION ATOMS=@phi-6" )
t10 = create_plumed_var( p, "t10", "TORSION ATOMS=@psi-6" )
t11 = create_plumed_var( p, "t11", "TORSION ATOMS=@phi-7" )
t12 = create_plumed_var( p, "t12", "TORSION ATOMS=@psi-7" )
t13 = create_plumed_var( p, "t13", "TORSION ATOMS=@phi-8" )
t14 = create_plumed_var( p, "t14", "TORSION ATOMS=@psi-8" )
t15 = create_plumed_var( p, "t15", "TORSION ATOMS=@phi-9" )
t16 = create_plumed_var( p, "t16", "TORSION ATOMS=@psi-9" )
t17 = create_plumed_var( p, "t17", "TORSION ATOMS=@phi-10" )
t18 = create_plumed_var( p, "t18", "TORSION ATOMS=@psi-10" )
t19 = create_plumed_var( p, "t19", "TORSION ATOMS=@phi-11" )
t20 = create_plumed_var( p, "t20", "TORSION ATOMS=@psi-11" )
t21 = create_plumed_var( p, "t21", "TORSION ATOMS=@phi-12" )
t22 = create_plumed_var( p, "t22", "TORSION ATOMS=@psi-12" )
t23 = create_plumed_var( p, "t23", "TORSION ATOMS=@phi-13" )
t24 = create_plumed_var( p, "t24", "TORSION ATOMS=@psi-13" )
t25 = create_plumed_var( p, "t25", "TORSION ATOMS=@phi-14" )
t26 = create_plumed_var( p, "t26", "TORSION ATOMS=@psi-14" )
t27 = create_plumed_var( p, "t27", "TORSION ATOMS=@phi-15" )
t28 = create_plumed_var( p, "t28", "TORSION ATOMS=@psi-15" )
t29 = create_plumed_var( p, "t29", "TORSION ATOMS=@phi-16" )
t30 = create_plumed_var( p, "t30", "TORSION ATOMS=@psi-16" )
t31 = create_plumed_var( p, "t31", "TORSION ATOMS=@phi-17" )
t32 = create_plumed_var( p, "t32", "TORSION ATOMS=@psi-17" )
# Read in the correct answers that were calculated directly using PLUMED
correct_torsions = np.loadtxt("colvar.ref")
# Open an output file
of = open("logfile", "w+")
# Now analyze the trajectory
for step in range(0,num_frames) :
of.write("RUNNING ANALYSIS FOR STEP " + str(step) + "\n" )
p.cmd("setStep",step )
p.cmd("setBox",box )
p.cmd("setMasses", masses )
p.cmd("setCharges", charges )
p.cmd("setPositions", traj[step])
p.cmd("setForces", forces )
p.cmd("setVirial", virial )
p.cmd("calc")
bias = np.zeros((1),dtype=np.float64)
p.cmd("getBias", bias )
variables = np.array([t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32]).ravel()
zeros = variables - correct_torsions[step,1:]
for data in zeros :
if abs(data)>1E-4 : of.write("MISMATCH BETWEEN VALUE FROM PLUMED AND VALUE FROM PYTHON")
of.close()
