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fortranMCMDpy.py
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fortranMCMDpy.py
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import ctypes
from numpy.ctypeslib import ndpointer
import numpy as np
import os, ase
class fortran_MC_MD:
def __init__(self, model_so):
if model_so.find("/") == 0:
self.model_lib = ctypes.CDLL(model_so, mode=ctypes.RTLD_GLOBAL)
else:
if 'PYMATNEST_PATH' in os.environ:
self.model_lib = ctypes.CDLL(os.environ['PYMATNEST_PATH']+"/"+model_so, mode=ctypes.RTLD_GLOBAL)
else:
self.model_lib = ctypes.CDLL(os.path.dirname(__file__)+"/"+model_so, mode=ctypes.RTLD_GLOBAL)
# ll_init_model
self.model_lib.ll_init_model_.argtypes = [ctypes.c_void_p, # N_params
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS") ] # params
# ll_init_config
self.model_lib.ll_init_config_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ctypes.c_void_p ] # Emax
# ll_eval_energy
self.model_lib.ll_eval_energy_.restype = ctypes.c_double
self.model_lib.ll_eval_energy_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS")] # cell
# ll_move_atom_1
self.model_lib.ll_move_atom_1_.restype = ctypes.c_int
self.model_lib.ll_move_atom_1_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ctypes.c_void_p, # d_i
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # d_pos
ctypes.c_void_p, # dE_max
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS") ] # dE
# ll_eval_forces
self.model_lib.ll_eval_forces_.restype = ctypes.c_double
self.model_lib.ll_eval_forces_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS")] # forces
if 'PYMATNEST_PATH' in os.environ:
self.lib = ctypes.CDLL(os.environ['PYMATNEST_PATH']+"/fortran_MC_MD.so")
else:
self.lib = ctypes.CDLL(os.path.dirname(__file__)+"/fortran_MC_MD.so")
# fortran_seed_size
self.lib.fortran_seed_size_.restype = ctypes.c_int
# fortran_set_seed
self.lib.fortran_set_seed_.argtypes = [ctypes.c_void_p, # n_seed
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS")] # seed
# fortran_MC_atom_velo
self.lib.fortran_mc_atom_velo_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # velo
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # masses
ctypes.c_void_p, # n_steps
ctypes.c_void_p, # step_size
ctypes.c_void_p, # nD
ctypes.c_void_p, # KEmax
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # final_KE
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # n_try
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS")] # n_accept
# fortran_MC_atom
self.lib.fortran_mc_atom_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # velo
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # masses
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ctypes.c_void_p, # n_steps
ctypes.c_void_p, # step_size_pos
ctypes.c_void_p, # step_size_velo
ctypes.c_void_p, # Emax
ctypes.c_void_p, # nD
ctypes.c_void_p, # fixN
ctypes.c_void_p, # wall
ctypes.c_void_p, # KEmax
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # final_E
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # n_try
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # n_accept
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS")] # n_accept_velo
# fortran_GMC_atom
self.lib.fortran_gmc_atom_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # masses
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ctypes.c_void_p, # n_steps
ctypes.c_void_p, # Emax
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # final_E
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # n_try
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # n_accept
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # d_pos
ctypes.c_void_p, # no_reverse
ctypes.c_void_p, # pert_ang
ctypes.c_void_p ] # debug
# fortran_MD_atom_NVE
self.lib.fortran_md_atom_nve_.argtypes = [ctypes.c_void_p, # N
ndpointer(ctypes.c_int, flags="C_CONTIGUOUS"), # Z
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # pos
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # vel
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # mass
ctypes.c_void_p, # n_extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # extra_data
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # cell
ctypes.c_void_p, # n_steps
ctypes.c_void_p, # timestep
ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), # final_E
ctypes.c_void_p] # debug
# MODEL ###############################################################################
def init_model(self, params):
n_params = ctypes.c_int(len(params))
self.model_lib.ll_init_model_(ctypes.byref(n_params), params)
def init_config(self, at, Emax):
n = ctypes.c_int(len(at))
Emax = ctypes.c_double(Emax)
self.model_lib.ll_init_config_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), at.get_positions(), at.get_cell()[:,:], ctypes.byref(Emax))
def eval_energy(self, at):
n = ctypes.c_int(len(at))
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data=np.zeros( (1) )
return self.model_lib.ll_eval_energy_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), at.get_positions(), ctypes.byref(n_extra_data_c), extra_data, at.get_cell()[:,:])
def move_atom_1(self, at, d_i, d_pos, dEmax):
n = ctypes.c_int(len(at))
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data=np.zeros( (1) )
d_i = ctypes.c_int(d_i)
dEmax = ctypes.c_double(dEmax)
dE = np.zeros( (1) )
pos = at.get_positions()
accept = self.model_lib.ll_move_atom_1_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), pos, ctypes.byref(n_extra_data_c), extra_data,
at.get_cell()[:,:], ctypes.byref(d_i), d_pos, ctypes.byref(dEmax), dE)
if accept > 0:
at.set_positions(pos)
if n_extra_data_c.value > 0:
at.arrays['ns_extra_data'][:,:] = extra_data
return (accept, dE[0])
def eval_forces(self, at, forces):
n = ctypes.c_int(len(at))
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data=np.zeros( (1) )
return self.model_lib.ll_eval_forces_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), at.get_positions(), ctypes.byref(n_extra_data_c), extra_data, at.get_cell()[:,:], forces)
# MC/MD WALK ###############################################################################
def seed_size(self):
return self.lib.fortran_seed_size_()
def set_seed(self, seed):
n_seed = ctypes.c_int(len(seed))
self.lib.fortran_set_seed_(ctypes.byref(n_seed), seed)
def MC_atom_walk_velo(self, at, n_steps, step_size, nD, KEmax):
n = ctypes.c_int(len(at))
n_steps = ctypes.c_int(n_steps)
step_size = ctypes.c_double(step_size)
nD = ctypes.c_int(nD)
KEmax = ctypes.c_double(KEmax)
velo = at.get_velocities()
n_try = np.zeros( (1), dtype=np.int32)
n_accept = np.zeros( (1), dtype=np.int32)
final_KE = np.zeros( (1), dtype=np.float64)
self.lib.fortran_mc_atom_velo_(ctypes.byref(n), velo, at.get_masses(),
ctypes.byref(n_steps), ctypes.byref(step_size),
ctypes.byref(nD),
ctypes.byref(KEmax), final_KE, n_try, n_accept)
at.set_velocities(velo)
return (n_try[0], n_accept[0], final_KE[0])
def MC_atom_walk(self, at, n_steps, step_size_pos, Emax, nD, fixN=0, wall=0.0, KEmax=-1.0, step_size_velo=None):
n = ctypes.c_int(len(at))
n_steps = ctypes.c_int(n_steps)
step_size_pos = ctypes.c_double(step_size_pos)
if step_size_velo is None:
step_size_velo_c = ctypes.c_double(0.0)
else:
step_size_velo_c = ctypes.c_double(step_size_velo)
Emax = ctypes.c_double(Emax)
KEmax = ctypes.c_double(KEmax)
nD = ctypes.c_int(nD)
fixN = ctypes.c_int(fixN)
wall = ctypes.c_double(wall)
pos = at.get_positions()
if step_size_velo is None:
velo = np.zeros( (1), dtype=np.float64 )
else:
velo = at.get_velocities()
n_try = np.zeros( (1), dtype=np.int32)
n_accept_pos = np.zeros( (1), dtype=np.int32)
n_accept_velo = np.zeros( (1), dtype=np.int32)
final_E = np.zeros( (1), dtype=np.float64)
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data=np.zeros( (1) )
self.lib.fortran_mc_atom_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), pos, velo, at.get_masses(), ctypes.byref(n_extra_data_c),
extra_data, at.get_cell()[:,:],
ctypes.byref(n_steps), ctypes.byref(step_size_pos), ctypes.byref(step_size_velo_c),
ctypes.byref(Emax), ctypes.byref(nD), ctypes.byref(fixN), ctypes.byref(wall), ctypes.byref(KEmax), final_E, n_try, n_accept_pos, n_accept_velo)
at.set_positions(pos)
if n_extra_data_c.value > 0:
at.arrays['ns_extra_data'][...] = extra_data
if step_size_velo is None:
return (n_try[0], n_accept_pos[0], final_E[0])
else:
at.set_velocities(velo)
return (n_try[0], n_accept_pos[0], n_accept_velo[0], final_E[0])
def GMC_atom_walk(self, at, n_steps, step_size, Emax, no_reverse=True, pert_ang=0.0, debug = 0):
n = ctypes.c_int(len(at))
n_steps = ctypes.c_int(n_steps)
Emax = ctypes.c_double(Emax)
debug = ctypes.c_int(debug)
if no_reverse:
no_reverse = ctypes.c_int(1)
else:
no_reverse = ctypes.c_int(0)
pert_ang = ctypes.c_double(pert_ang)
pos = at.get_positions()
d_pos = step_size*at.arrays['GMC_direction']
n_try = np.zeros( (1), dtype=np.int32)
n_accept = np.zeros( (1), dtype=np.int32)
final_E = np.zeros( (1), dtype=np.float64)
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data=np.zeros( (1) )
self.lib.fortran_gmc_atom_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32), pos, at.get_masses(), ctypes.byref(n_extra_data_c),
extra_data, at.get_cell()[:,:], ctypes.byref(n_steps), ctypes.byref(Emax), final_E, n_try, n_accept, d_pos, ctypes.byref(no_reverse), ctypes.byref(pert_ang), ctypes.byref(debug))
at.set_positions(pos)
at.arrays['GMC_direction'][:,:] = d_pos / np.linalg.norm(d_pos)
if n_extra_data_c.value > 0:
at.arrays['ns_extra_data'][...] = extra_data
return (n_try[0], n_accept[0], final_E[0])
def MD_atom_NVE_walk(self, at, n_steps, timestep, debug):
n = ctypes.c_int(len(at))
n_steps = ctypes.c_int(n_steps)
timestep = ctypes.c_double(timestep)
pos = at.get_positions()
vel = at.get_velocities()
debug = ctypes.c_int(debug)
final_E = np.zeros( (1), dtype=np.float64)
if 'ns_extra_data' in at.arrays:
n_extra_data_c = ctypes.c_int(at.arrays['ns_extra_data'].size/len(at))
extra_data = at.arrays['ns_extra_data']
else:
n_extra_data_c = ctypes.c_int(0)
extra_data= np.zeros( (1) )
self.lib.fortran_md_atom_nve_(ctypes.byref(n), at.get_atomic_numbers().astype(np.int32),
pos, vel, at.get_masses(), ctypes.byref(n_extra_data_c), extra_data, at.get_cell()[:,:],
ctypes.byref(n_steps), ctypes.byref(timestep), final_E, ctypes.byref(debug))
at.set_positions(pos)
at.set_velocities(vel)
if n_extra_data_c.value > 0:
at.arrays['ns_extra_data'][...] = extra_data
return final_E[0]