def opt(T=350):
A = read('packed.gen')
# A = press_mol(A)
write_gulp_in(A, runword='opti conv qiterative ', T=T, lib='reax')
print('\n- running gulp optimize ...')
system('gulp<inp-gulp>gulp.out')
xyztotraj('his.xyz', mode='w')
def nvt_wt(T=350,
time_step=0.1,
tot_step=100,
gen='packed.gen',
mode='w',
wt=25):
A = read(gen, index=-1)
write_gulp_in(A,
runword='md conv qiterative ',
T=T,
time_step=time_step,
tot_step=tot_step,
lib='reax')
print('\n- running gulp nvt ...')
system('nohup gulp<inp-gulp>gulp.out 2>&1 &')
thread = popen('ps -aux | grep "gulp"')
lines = thread.readlines()
time.sleep(wt)
for line in lines:
l = line.split()
if l[7] == 'R+' or l[7] == 'R':
system('kill %s' % l[1])
xyztotraj('his.xyz', mode=mode)
def npt(T=350, time_step=0.1, tot_step=10.0):
A = read('packed.gen')
write_gulp_in(A,
runword='md conp',
T=T,
time_step=time_step,
tot_step=tot_step,
lib='reax')
system('gulp<inp-gulp>gulp.out')
xyztotraj('his.xyz')
def nvt(T=350,time_step=0.1,tot_step=5000,gen='siesta.traj',index=-1,mode='w'):
''' a gulp MD run '''
A = read(gen,index=index)
write_gulp_in(A,runword='md qiterative conv',
T=T,
time_step=time_step,
tot_step=tot_step,
lib='reax')
print('\n- running gulp nvt ...')
system('gulp<inp-gulp>gulp.out')
xyztotraj('his.xyz',mode=mode)
def nvt(T=350, time_step=0.1, tot_step=100, gen='packed.gen', mode='w'):
A = read(gen, index=-1)
write_gulp_in(A,
runword='md qiterative conv',
T=T,
time_step=time_step,
tot_step=tot_step,
lib='reax')
print('\n- running gulp nvt ...')
system('gulp<inp-gulp>gulp.out')
xyztotraj('his.xyz', mode=mode)
def x(mode='w'):
xyztotraj('his.xyz',mode=mode)