atom1 = Atom()
atom2 = Atom()
atom1.set_pos(0.0, 0.0, 0.0)
atom1.set_id(1)
atom1.set_sid(sid1)
asys.add_atom(atom1)
atom2.set_pos(0.5, 0.0, 0.0)
atom2.set_id(2)
atom2.set_sid(sid2)
asys.add_atom(atom2)
hmin = rmin / (2 * rcut)
hd = (0.5 - hmin) / nsmpl
os.system('cp pmdini pmdorig')
fout = open('out.2body', 'w')
for ip in range(nsmpl + 1):
print '.',
d = hmin + hd * ip
asys.atoms[1].pos[0] = d
asys.write_pmd('pmdini')
os.system(pmdexec + ' > out.pmd')
epot = get_epot('out.pmd')
fout.write(' {0:12.3f} {1:22.14e}\n'.format(d * 2 * rcut, epot))
fout.close()
#....restore pmdini
os.system('cp pmdorig pmdini')
print ' program done.'
asys.add_atom(atom1)
hd= distance/(alc*2)
atom2= Atom()
atom2.set_pos(hd,0.0,0.0)
atom2.set_id(2)
asys.add_atom(atom2)
atom3= Atom()
atom3.set_pos(0.0,0.0,0.0)
atom3.set_id(3)
asys.add_atom(atom3)
da = (amax-amin)/nsmpl
fout= open('out.3body','w')
for ip in range(nsmpl+1):
print('.',end='')
ang= amin +da*ip
x= hd*np.cos(ang/180*np.pi)
y= hd*np.sin(ang/180*np.pi)
asys.atoms[2].pos[0] = x
asys.atoms[2].pos[1] = y
asys.write_pmd('pmdini')
os.system(pmdexec+' > out.pmd')
apot= get_apot('out.pmd')
fout.write(' {0:12.3f} {1:22.14e}\n'.format(ang,apot))
fout.close()
print(' program done.')
fcmat = np.zeros((natme, natme, 3, 3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos = np.array(sysext.atoms[ia].pos)
for ixyz in range(3):
fam = np.zeros((natme, 3))
fap = np.zeros((natme, 3))
for kd in (-1, 1):
sysext.atoms[ia].pos[:] = ppos[:]
dx = np.zeros(3)
dx[ixyz] = kd * displace
hdx = cart2h(dx, hext)
sysext.atoms[ia].pos[:] += hdx
#...perform pmd here
sysext.write_pmd('pmdini')
os.system(pmdexec + ' > out.pmd')
#os.system('cp frc0000 frc0000-{0:1d}-{1:1d}-{2:1d}'.format(ia,ixyz,kd))
#...obtain forces on atoms
ff = open('frc0000', 'r')
ntmp = int(ff.readline().split()[0])
for ja in range(natme):
data = ff.readline().split()
if kd == -1:
fam[ja, 0] = float(data[0])
fam[ja, 1] = float(data[1])
fam[ja, 2] = float(data[2])
else:
fap[ja, 0] = float(data[0])
fap[ja, 1] = float(data[1])
fap[ja, 2] = float(data[2])
# Make directories for the calculation of those POSCARS
poscars= glob.glob("POSCAR-[0-9]??")
n= 0
for poscar in poscars:
n+=1
dname="disp-{0:03d}".format(n)
os.system("mkdir -p {0}".format(dname))
os.system("cp {0} {1}/POSCAR".format(poscar,dname))
print("processing {0}...".format(dname))
# Prepare pmd calculation
psystmp= NAPSystem()
psystmp.read_POSCAR(poscar)
os.system("cp in.* {0}/".format(dname))
if execname == "pmd":
psystmp.write_pmd("{0}/pmdini".format(dname))
elif execname == "smd":
psystmp.write_pmd("{0}/smd0000".format(dname))
os.system("cd {0}/; {1}/{2} > out.{2}; cd ..".format(dname,pmddir,execname))
# Make FORCE_SETS file from the pmd results
natm= int(disp['natom'])
ndisps= len(disp['displacements'])
with open('FORCE_SETS','w') as f:
f.write("{0:d}\n".format(natm))
f.write("{0:d}\n".format(ndisps))
n=0
for ds in disp['displacements']:
n+=1
f.write("\n")
f.write("{0:d}\n".format(n))
atom1 = Atom()
atom2 = Atom()
atom1.set_pos(0.0, 0.0, 0.0)
atom1.set_id(1)
atom1.set_sid(sid1)
asys.add_atom(atom1)
atom2.set_pos(0.5, 0.0, 0.0)
atom2.set_id(2)
atom2.set_sid(sid2)
asys.add_atom(atom2)
hmin = rmin / (2 * rcut)
hd = (0.5 - hmin) / nsmpl
os.system("cp pmd0000 pmd0000.orig")
fout = open("out.2body", "w")
for ip in range(nsmpl + 1):
print ".",
d = hmin + hd * ip
asys.atoms[1].pos[0] = d
asys.write_pmd("pmd0000")
os.system(pmdexec + " > out.pmd")
epot = get_epot("out.pmd")
fout.write(" {0:12.3f} {1:22.14e}\n".format(d * 2 * rcut, epot))
fout.close()
# ....restore pmd0000
os.system("cp pmd0000.orig pmd0000")
print " program done."
fcmat= np.zeros((natme,natme,3,3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos= np.array(sysext.atoms[ia].pos)
for ixyz in range(3):
fam= np.zeros((natme,3))
fap= np.zeros((natme,3))
for kd in (-1,1):
sysext.atoms[ia].pos[:]= ppos[:]
dx= np.zeros(3)
dx[ixyz]= kd*displace
hdx= cart2h(dx,hext)
sysext.atoms[ia].pos[:] += hdx
#...perform pmd here
sysext.write_pmd('pmd0000')
os.system(pmdexec+' > out.pmd')
#os.system('cp frc0000 frc0000-{0:1d}-{1:1d}-{2:1d}'.format(ia,ixyz,kd))
#...obtain forces on atoms
ff= open('frc0000','r')
ntmp= int(ff.readline().split()[0])
for ja in range(natme):
data= ff.readline().split()
if kd == -1:
fam[ja,0]= float(data[0])
fam[ja,1]= float(data[1])
fam[ja,2]= float(data[2])
else:
fap[ja,0]= float(data[0])
fap[ja,1]= float(data[1])
fap[ja,2]= float(data[2])
fcmat= np.zeros((natme,natme,3,3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos= np.array(sysext.atoms[ia].pos)
for ixyz in range(3):
fam= np.zeros((natme,3))
fap= np.zeros((natme,3))
for kd in (-1,1):
sysext.atoms[ia].pos[:]= ppos[:]
dx= np.zeros(3)
dx[ixyz]= kd*displace
hdx= cart2h(dx,hext)
sysext.atoms[ia].pos[:] += hdx
#...perform pmd here
sysext.write_pmd('pmdini')
os.system(pmdexec+' > out.pmd')
#os.system('cp frc0000 frc0000-{0:1d}-{1:1d}-{2:1d}'.format(ia,ixyz,kd))
#...obtain forces on atoms
ff= open('frc0000','r')
ntmp= int(ff.readline().split()[0])
for ja in range(natme):
data= ff.readline().split()
if kd == -1:
fam[ja,0]= float(data[0])
fam[ja,1]= float(data[1])
fam[ja,2]= float(data[2])
else:
fap[ja,0]= float(data[0])
fap[ja,1]= float(data[1])
fap[ja,2]= float(data[2])
asys.add_atom(atom1)
hd= distance/(alc*2)
atom2= Atom()
atom2.set_pos(hd,0.0,0.0)
atom2.set_id(2)
asys.add_atom(atom2)
atom3= Atom()
atom3.set_pos(0.0,0.0,0.0)
atom3.set_id(3)
asys.add_atom(atom3)
da = (amax-amin)/nsmpl
fout= open('out.3body','w')
for ip in range(nsmpl+1):
print '.',
ang= amin +da*ip
x= hd*np.cos(ang/180*np.pi)
y= hd*np.sin(ang/180*np.pi)
asys.atoms[2].pos[0] = x
asys.atoms[2].pos[1] = y
asys.write_pmd('pmd0000')
os.system(pmdexec+' > out.pmd')
apot= get_apot('out.pmd')
fout.write(' {0:12.3f} {1:22.14e}\n'.format(ang,apot))
fout.close()
print ' program done.'
