def makeFiles(sg):
global cnt
# mkdir
os.system('mkdir -p ./lammps/%i' % cnt)
#ff
FF = read_ff_vary('/stokes/yuchen/PyMD/FORCEFIELDS/JC/TIP4P2005_q%i' % q,
config['ci'],
ep,
sg,
bonded=True)
write_forcefield(
'./lammps/%i/in.forcefield' % cnt,
'lj/cut/tip4p/long 1 2 1 1 0.1546 %.1f %.1f' % (rc, rc), # functional
atoms,
bonds,
angles,
FF) # input data
# generate in.lammpsdata, directly cpy
os.system('cp ./in.lammpsdata ./lammps/%i/' % cnt)
# generate in.simulation
os.system('cp ./in.simulation ./lammps/%i/' % cnt)
# generate run.sh
os.system('cp ./run.sh ./lammps/')
cnt += 1
def tgFunc(sg, ep):
global cnt, obs, data
# ff
FF = read_ff_vary('/stokes/yuchen/PyMD/FORCEFIELDS/JC/TIP4P2005_q%i' % q,
config['ele'],
10**ep,
sg,
bonded=True)
write_forcefield(
'%s/in.forcefield' % loc,
'lj/cut/tip4p/long 1 2 1 1 0.1546 %.1f %.1f' % (rc, rc), # functional
atoms,
bonds,
angles,
FF) # input data
# lammpsdata, simulation, lambds
os.system('cp in.lammpsdata %s' % loc)
os.system('cp in.simulation %s' % loc)
os.system('cp in.lambdas %s' % loc)
# run system, pp
os.chdir(loc)
os.system('mpirun -np 5 lmp_mpi -in in.simulation')
os.chdir('../../')
rio, cn = readRDF('%s/NaO.rdf' % loc)
fN = transform(rio, tg)
os.system('mkdir ./lammps/%i' % cnt)
os.system('cp %s/* ./lammps/%i' % (loc, cnt))
os.system('rm -rf %s/*' % loc)
# if this function is called, then use global vaiable to record
obs.append([cnt + 1, rio, sg, ep])
obsArr = np.array(obs)
obsErArr = obsArr.copy()
obsErArr[:, 1] = -1 * transform(obsErArr[:, 1], tg)
data['obs'] = obsArr
data['obsEr'] = obsErArr
data = {**config, **data}
pickle.dump(data, open('data.pc', 'wb'))
cnt += 1
return fN