dimer = s22.create_s22_system('Water_dimer')
dimer.center(vacuum=5.0)
# rotate the second water mol into the same x plane as
# the first one, to make the potential curve easier to make
center = dimer[0].position
h = dimer[3].position[1]-dimer[0].position[1]
l = np.linalg.norm(dimer[0].position - dimer[3].position)
angle = np.arcsin(h/l)
dimer.rotate('-z',a=angle,center=center)
nsys = dimer[:3].copy()
nsys.set_positions(dimer[:3].get_positions() + (2.,2.,0))
trimer = dimer + nsys # 3 mols now
qmidx = 3
calc_qm = GPAW(h=0.20,mode='lcao',basis={None:'dzp'},txt='simpletest.txt')
eF = np.zeros((3,2))
calc_mm = CALC_SCME(trimer[qmidx:])
trimer.set_calculator(ase_qmscme(trimer, qmidx=3,calc_qm=calc_qm,
calc_mm=calc_mm,qm_cell=trimer.get_cell()))
Etot = trimer.get_potential_energy()
print '\n################################## #'
print '########### TOTAL ENERGY ######### #'
print Etot
print '################################## #'
if step > -1: # if you accidentally break the script before done
dimer.center(vacuum=5.0)
qm_cell = dimer.get_cell()
dist = np.linalg.norm(dimer[0].position - dimer[3].position)
extra = dimer[0:3].copy()
extra.translate([100, 0, 0])
full_sys = dimer + extra
calc_mm = CALC_SCME(full_sys[qmidx:])
full_sys.set_cell([200, 200, 200])
calc_qm = GPAW(h=0.20, mode="lcao", xc="PBE", basis={None: "dzp"}, txt=path + "dimer_%2.4f.txt" % dist)
full_sys.set_calculator(
ase_qmscme(
full_sys,
qmidx=3,
calc_qm=calc_qm,
calc_mm=calc_mm,
qm_cell=qm_cell,
LJ_qm=LJ_qm.T,
LJ_mm=LJ_mm.T,
qm_fixed=True,
)
)
# try:
Epot = full_sys.get_potential_energy()
print "Step: %5.2f, dist: %5.2f, Epot: %5.2f" % (step, dist, Epot)
# except:
# Epot = float('Nan')
if rank == MASTER:
f.write("%24s%24s%24s\n" % (dist, Epot, Epot - Esingle))
print ("%24s%24s%24s\n" % (dist, Epot, Epot - Esingle))
for step in range(0, 5, 1):
for mol1 in range(3):
dimer[mol1].x -= 0.05*2
for mol2 in range(3,6):
dimer[mol2].x += 0.05*2
if step > -1: # if you accidentally break the script before done
dimer.center(vacuum=5.0)
qm_cell = dimer.get_cell()
dist = np.linalg.norm(dimer[0].position - dimer[3].position)
extra = dimer[0:3].copy()
extra.translate([100,0,0])
full_sys = dimer + extra
calc_mm = CALC_SCME(full_sys[qmidx:])
full_sys.set_cell([200,200,200])
calc_qm = GPAW(h=0.20,mode='lcao',xc='PBE',
basis={None:'dzp'},txt=path+'singleproc_dimer_%2.4f.txt'%dist)
full_sys.set_calculator(ase_qmscme(full_sys, qmidx=3,calc_qm=calc_qm,
calc_mm=calc_mm,qm_cell=qm_cell,
LJ_qm=LJ_qm.T, LJ_mm=LJ_mm.T, qm_fixed = True))
#try:
Epot = full_sys.get_potential_energy()
print 'Step: %5.2f, dist: %5.2f, Epot: %5.2f'%(step, dist,Epot)
#except:
# Epot = float('Nan')
if rank == MASTER:
f.write('%24s%24s%24s\n' %(dist,Epot,Epot-Esingle))
print('%24s%24s%24s\n' %(dist,Epot,Epot-Esingle))
