def pd_init(self):
self.net.net.write(self.net.name + '_init.txyz', ftype='txyz')
self.pd = pydlpoly.pydlpoly(self.net.name)
self.pd.control["cut"] = 0.5
self.pd.control["no link"] = " "
self.pd.setup(xyz=self.net.name + "_init.txyz",
key=self.net.name + ".key",
local=True,
bcond=3)
return
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import pydlpoly
import molsys
# initialize a pydlpoly instance
m = molsys.mol()
m.read("bdc_0opt.mfpx")
m.addon("ff")
m.ff.read("bdc_0")
pd = pydlpoly.pydlpoly("test")
pd.control["shift"] = ""
pd.control["spme"] = "precision 1.0d-6"
pd.setup(mol=m, local=False)
# set field
pd.set_efield([0.00, 0.0, 0.0], use_ref=False, const_D=False)
pd.set_atoms_moved()
pd.calc_energy_force()
# equilibrate temperature
pd.MD_init("equil", T=150, ensemble="nvt", thermo="ber", relax=[0.2])
pd.MD_run(100000, printout=100)
# sampling
pd.MD_init("cons",
T=150,
ensemble="nvt",
from molsys.util import ff2pydlpoly
import cma
# specify a name
name = "ph-ph"
# initialize a molsys object
m = molsys.mol.fromFile("ph-ph.mfpx")
# add ff addon and read in the fpar and ric file
m.addon("ff")
m.ff.read(name, fit=True)
# setup pydlpoly
wm = ff2pydlpoly.wrapper(m)
pd = pydlpoly.pydlpoly(name)
pd.setup(web=wm)
# initialize ric addon, need to be done after pydlpoly setup
m.addon("ric")
m.ric.setup_rics(full=False)
# initialize ric_fit objective
ric = ric_fit.ric_fit(only_diag=False)
# initialize FFgen
ff = ff_gen.ff_gen(name, pd, objective=ric, minimize=True)
# set maxiter and inititialize CMA-ES on the problem
miter = 10
es = cma.CMAEvolutionStrategy(ff.initials, 0.2, {
import pydlpoly
pd = pydlpoly.pydlpoly("dut49")
# enforce triclinic -> otherwise all is orthorombic
pd.setup(bcond=3)
# do a first round of NVT with a quick/fast Berendsen Thermostat
pd.MD_init("equil_NVT", T=300.0, p=0.001, startup=True, ensemble="nvt", thermo="ber", relax=(0.1,))
pd.MD_run(20000)
# now start up NsT with a Hoover thermostat .. first for equlibrating
pd.MD_init("equil_NPT", T=300.0, p=0.001, ensemble="npt", thermo="hoover", relax=(1.0, 2.0))
pd.MD_run(1000000)
# finally sample NsT with a Hoover thermostat
pd.MD_init("sample_NPT", T=300.0, p=0.001, ensemble="npt", thermo="hoover", relax=(1.0, 2.0), traj=["cell", "xyz"], tnstep=10)
pd.MD_run(5000000)