def getbol(self):
maindir = tl.pwd()
tl.mkcd('bol')
self.runscf()
self.runnscf()
self.runw()
tl.cd(maindir)
def checkMinimize(self):
import yaml
data = yaml.load(open('disp.yaml').read())
disps = [map(float, a['direction']) for a in data['displacements']]
maindir = pwd()
dirs = ls('dirs/dir_*')
ii = 0
L = np.linalg.norm
# d,p,d1,p1=self.m.rot
out = open('ccos.txt', 'w')
for dir in dirs:
cd(dir)
f = open('dump.force')
for i in range(9):
f.next()
for b in range(ii):
f.next()
line = f.next()
line = line.split()
force = np.array(map(float, line[1:4]))
# force=RotateVector(force,d1,-p1)
# force=RotateVector(force,d,-p)
d = disps[i]
ccos = force.dot(d) / L(force) / L(d)
ii += 1
print >> out, "%d\t%f" % (ii, ccos)
cd(maindir)
def getPhonons(self):
maindir = tl.pwd()
tl.mkcd('phonons')
self.runscf()
self.runph()
self.collect()
tl.cd(maindir)
def getvasprun(self, files):
m = self.m
maindir = pwd()
if m.engine == "vasp":
calculator = self.getVaspRun_vasp
elif m.engine == "lammps":
calculator = self.getVaspRun_lammps
self.jm = jobManager()
for file in files:
print(file)
dir = "dirs/dir_" + file
mkdir(dir)
mv(file, dir + '/POSCAR')
cd(dir)
calculator()
cd(maindir)
self.jm.run()
if m.th:
mkdir(m.pbsname)
self.thcode(files, m.pbsname)
cp("dirs", m.pbsname)
passthru("tar zcf %s.tar.gz %s" % (m.pbsname, m.pbsname))
print('start check')
self.jm.check()
if m.engine == "lammps1":
from multiprocessing.dummy import Pool
pool = Pool()
pool.map_async(lammpsvasprun, files)
pool.close()
pool.join()
def checkMinimize(self):
import yaml
data = yaml.load(open('disp.yaml').read())
disps = [map(float, a['direction']) for a in data['displacements']]
maindir = pwd()
dirs = ls('dirs/dir_*')
ii = 0
L = np.linalg.norm
# d,p,d1,p1=self.m.rot
out = open('ccos.txt', 'w')
for dir in dirs:
cd(dir)
f = open('dump.force')
for i in range(9):
f.next()
for b in range(ii):
f.next()
line = f.next()
line = line.split()
force = np.array(map(float, line[1:4]))
# force=RotateVector(force,d1,-p1)
# force=RotateVector(force,d,-p)
d = disps[i]
ccos = force.dot(d) / L(force) / L(d)
ii += 1
print >> out, "%d\t%f" % (ii, ccos)
cd(maindir)
def getVaspRun_vasp(self):
m = self.m
if m.isym:
sym = "ISYM = 1"
else:
sym = "ISYM = 0"
if m.ispin:
spin = "ISPIN =2"
else:
spin = ""
s = """SYSTEM=calculate energy
PREC = High
IBRION = 8
ENCUT = %f
EDIFF = 1.0e-8
ISMEAR = %d; SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
ADDGRID = .TRUE.
LWAVE = .FALSE.
LCHARG = .FALSE.
%s
%s
""" % (self.m.ecut, m.ismear, sym, spin)
s = s.replace(r'^\s+', '')
tl.write(s, 'INCAR')
m = self.m
m.writePOTCAR()
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, m.ekpoints))
s = s.replace(r'^\s+', '')
tl.write(s, 'KPOINTS')
if 'jm' in self.__dict__:
from aces.jobManager import pbs
path = tl.pwd()
if m.queue == "q3.4":
pb = pbs(queue=m.queue,
nodes=12,
procs=4,
disp=m.pbsname,
path=path,
content=config.mpirun + " 48 " + config.vasp +
' >log.out')
else:
pb = pbs(queue=m.queue,
nodes=4,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 48 " + config.vasp +
' >log.out')
self.jm.reg(pb)
else:
tl.shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def getvasprun(self, files):
m = self.m
maindir = pwd()
if m.engine == "vasp":
calculator = self.getVaspRun_vasp
elif m.engine == "lammps":
calculator = self.getVaspRun_lammps
self.jm = jobManager()
for file in files:
print(file)
dir = "dirs/dir_" + file
mkdir(dir)
mv(file, dir + '/POSCAR')
cd(dir)
calculator()
cd(maindir)
self.jm.run()
if m.th:
mkdir(m.pbsname)
self.thcode(files, m.pbsname)
cp("dirs", m.pbsname)
passthru("tar zcf %s.tar.gz %s" % (m.pbsname, m.pbsname))
print('start check')
self.jm.check()
if m.engine == "lammps1":
from multiprocessing.dummy import Pool
pool = Pool()
pool.map_async(lammpsvasprun, files)
pool.close()
pool.join()
def run(self):
old = tl.pwd()
for job in self.jobs:
tl.cd(job.path)
job.writepbs()
job.submit()
tl.cd(old)
def getbol(self):
maindir = tl.pwd()
tl.mkcd('bol')
self.runscf()
self.runnscf()
self.runw()
tl.cd(maindir)
def getPhonons(self):
maindir = tl.pwd()
tl.mkcd('phonons')
self.runscf()
self.runph()
self.collect()
tl.cd(maindir)
def __init__(self):
"""
while not os.path.exists('app.json'):
time.sleep(1)
print pwd()+'/app.json'
"""
if tl.exists('app.json'):
opt = tl.loadjson('app.json')
elif tl.exists('../app.json'):
opt = tl.loadjson('../app.json')
elif tl.exists('../../app.json'):
opt = tl.loadjson('../../app.json')
elif tl.exists('../../../app.json'):
opt = tl.loadjson('../../../app.json')
else:
tl.exit('app.json lost!')
species = opt['species']
s = im('aces.materials.%s' % species)
m = s.structure(opt)
self.m = m
m.home = tl.pwd()
assert m.home != ''
Runner = im('aces.runners.%s' % m.runner)
self.runner = Runner.runner(m)
def run(self):
old = tl.pwd()
for job in self.jobs:
tl.cd(job.path)
job.writepbs()
job.submit()
tl.cd(old)
def dyinput(self):
m = self.m
f = open('in.dy', 'w')
print >> f, "STRUCTURE FILE POSCAR"
print >> f, tl.pwd() + "/POSCAR"
print >> f, "FORCE SETS"
print >> f, tl.pwd() + "/FORCE_SETS"
# print >>f,"STRUCTURE FILE OUTCAR"
# print >>f,pwd()+"/dynaphopy.lammpstrj"
print >> f, "SUPERCELL MATRIX PHONOPY"
print >> f, " %d 0 0 \n 0 %d 0\n 0 0 %d" % tuple(m.supercell)
print >> f, "BANDS"
bp = m.bandpath
bpp = m.bandpoints
for i in range(len(bp) - 1):
u = "%s %s" % (tl.toString(bpp[bp[i]],
','), tl.toString(bpp[bp[i + 1]], ','))
print >> f, u
f.close()
def dyinput(self):
m = self.m
f = open('in.dy', 'w')
print >> f, "STRUCTURE FILE POSCAR"
print >> f, tl.pwd() + "/POSCAR"
print >> f, "FORCE SETS"
print >> f, tl.pwd() + "/FORCE_SETS"
# print >>f,"STRUCTURE FILE OUTCAR"
# print >>f,pwd()+"/dynaphopy.lammpstrj"
print >> f, "SUPERCELL MATRIX PHONOPY"
print >> f, " %d 0 0 \n 0 %d 0\n 0 0 %d" % tuple(m.supercell)
print >> f, "BANDS"
bp = m.bandpath
bpp = m.bandpoints
for i in range(len(bp) - 1):
u = "%s %s" % (tl.toString(bpp[bp[i]], ','),
tl.toString(bpp[bp[i + 1]], ','))
print >> f, u
f.close()
def getPotName(self):
maindir = tl.pwd()
tl.cd(config.qepot)
files = tl.ls("*")
tl.cd(maindir)
import re
q = [re.split("[_\.]", a)[0].capitalize() for a in files]
u = {}
for i, v in enumerate(q):
u[v] = files[i]
return u
def getPotName(self):
maindir = tl.pwd()
tl.cd(config.qepot)
files = tl.ls("*")
tl.cd(maindir)
import re
q = [re.split("[_\.]", a)[0].capitalize() for a in files]
u = {}
for i, v in enumerate(q):
u[v] = files[i]
return u
def getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(
queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(
queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def runSPOSCAR(self):
m = self.m
maindir = pwd()
file = "SPOSCAR"
dir = "dir_" + file
mkdir(dir)
cp(file, dir + '/POSCAR')
cd(dir)
if m.engine == "vasp":
self.getVaspRun_vasp()
if m.engine == "lammps":
self.getVaspRun_lammps()
cd(maindir)
def getepw(self):
m = self.m
maindir = tl.pwd()
tl.mkcd('epw')
"""为了保证q+k也在k的格点上，必须要求qs*cell*[nk1,nk2,nk3]为整数，即nk=N*nq
否则可能出现Error in routine createkmap (1):
"""
u = np.array(m.ekpoints) / np.array(m.kpoints)
assert np.allclose(np.floor(u + .5), u, rtol=0.01)
self.runscf()
self.runnscf()
self.runepw()
tl.cd(maindir)
def runSPOSCAR(self):
m = self.m
maindir = pwd()
file = "SPOSCAR"
dir = "dir_" + file
mkdir(dir)
cp(file, dir + '/POSCAR')
cd(dir)
if m.engine == "vasp":
self.getVaspRun_vasp()
if m.engine == "lammps":
self.getVaspRun_lammps()
cd(maindir)
def getVaspRun_lammps(self):
m = self.m
if 'jm' in self.__dict__:
path = pwd()
pb = pbs(queue=m.queue,
nodes=1,
procs=4,
disp=m.pbsname,
path=path,
content=config.python + vasprun.__file__ + ' >log.out')
self.jm.reg(pb)
else:
shell_exec(config.python + vasprun.__file__ + ' >log.out')
def ineq(m):
now = tl.pwd()
species = m.species
if not (species in ["CN-small"]):
return 0.0
tl.cd('minimize')
tl.mkdir('nonequ')
tl.cd('nonequ')
ie = inequality()
nonequ5 = ie.run()
tl.cd(now)
return nonequ5
def getepw(self):
m = self.m
maindir = tl.pwd()
tl.mkcd('epw')
"""为了保证q+k也在k的格点上，必须要求qs*cell*[nk1,nk2,nk3]为整数，即nk=N*nq
否则可能出现Error in routine createkmap (1):
"""
u = np.array(m.ekpoints) / np.array(m.kpoints)
assert np.allclose(np.floor(u + .5), u, rtol=0.01)
self.runscf()
self.runnscf()
self.runepw()
tl.cd(maindir)
def ineq(m):
now = tl.pwd()
species = m.species
if not (species in ["CN-small"]):
return 0.0
tl.cd('minimize')
tl.mkdir('nonequ')
tl.cd('nonequ')
ie = inequality()
nonequ5 = ie.run()
tl.cd(now)
return nonequ5
def getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def creatmini(self, m):
print('creatmini')
m.home = pwd()
assert m.home != ''
mkdir('minimize')
cd('minimize')
minimize_input(m)
write(time.strftime('%Y-%m-%d %H:%M:%S'), 'done')
cd('..')
if m.engine == "lammps":
return m.dump2POSCAR(m.home + '/minimize/range')
else:
return io.read(m.home + '/minimize/CONTCAR')
def getVaspRun_lammps(self):
m = self.m
if 'jm' in self.__dict__:
path = pwd()
pb = pbs(
queue=m.queue,
nodes=1,
procs=4,
disp=m.pbsname,
path=path,
content=config.python + vasprun.__file__ + ' >log.out')
self.jm.reg(pb)
else:
shell_exec(config.python + vasprun.__file__ + ' >log.out')
def tDisorder():
# disorder degree*/
now = tl.pwd()
tl.cd('minimize')
tl.mkcd('disorder')
disorderLine = tl.shell_exec(
"cp %s" % SRCHOME + "/in.disorder .;" + config.lammps +
" <in.disorder 2>err 1>log;tail -1 disorder.txt 2>err;")
k = disorderLine.split()[1:3]
if len(k) == 1:
k.append("")
disorder, rd = k
tl.cd(now)
return (disorder, rd)
def tDisorder():
# disorder degree*/
now = tl.pwd()
tl.cd('minimize')
tl.mkcd('disorder')
disorderLine = tl.shell_exec(
"cp %s" %
SRCHOME +
"/in.disorder .;" +
config.lammps +
" <in.disorder 2>err 1>log;tail -1 disorder.txt 2>err;")
k = disorderLine.split()[1:3]
if len(k) == 1:
k.append("")
disorder, rd = k
tl.cd(now)
return (disorder, rd)
def creatmini(self, dir):
cur = tl.pwd()
tl.mkdir(dir)
tl.cd(dir)
minimize_input(self.m)
tl.cd(cur)
def creatmini(self, dir):
cur = tl.pwd()
tl.mkdir(dir)
tl.cd(dir)
minimize_input(self.m)
tl.cd(cur)
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-18 22:01:52
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-18 22:02:30
from os.path import realpath, dirname, basename
from aces.tools import pwd, exists
SRCHOME = dirname(realpath(__file__))
def checkParent(dir, n=0):
if n == 5:
raise Exception('error when find sub.py')
if not exists(dir + '/sub.py'):
dir = realpath(dir + '/..')
return checkParent(dir, n + 1)
else:
return dir
PROJHOME = checkParent(pwd())
PROJNAME = basename(PROJHOME)
def getVaspRun_vasp(self):
m = self.m
if m.isym:
sym = "ISYM = 1"
else:
sym = "ISYM = 0"
if m.ispin:
spin = "ISPIN =2"
else:
spin = ""
s = """SYSTEM=calculate energy
PREC = High
IBRION = 8
ENCUT = %f
EDIFF = 1.0e-8
ISMEAR = %d; SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
ADDGRID = .TRUE.
LWAVE = .FALSE.
LCHARG = .FALSE.
%s
%s
""" % (self.m.ecut, m.ismear, sym, spin)
s = s.replace(r'^\s+', '')
tl.write(s, 'INCAR')
m = self.m
m.writePOTCAR()
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, m.ekpoints))
s = s.replace(r'^\s+', '')
tl.write(s, 'KPOINTS')
if 'jm' in self.__dict__:
from aces.jobManager import pbs
path = tl.pwd()
if m.queue == "q3.4":
pb = pbs(
queue=m.queue,
nodes=12,
procs=4,
disp=m.pbsname,
path=path,
content=config.mpirun +
" 48 " +
config.vasp +
' >log.out')
else:
pb = pbs(
queue=m.queue,
nodes=4,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun +
" 48 " +
config.vasp +
' >log.out')
self.jm.reg(pb)
else:
tl.shell_exec(
config.mpirun +
" %s " %
m.cores +
config.vasp +
' >log.out')
from os.path import *
from aces.tools import pwd, exists
import sys
SRCHOME = dirname(realpath(__file__))
def checkParent(dir, n=0):
if n == 5: raise Exception('error when find sub.py')
if not exists(dir + '/sub.py'):
dir = realpath(dir + '/..')
return checkParent(dir, n + 1)
else:
return dir
PROJHOME = checkParent(pwd())
PROJNAME = basename(PROJHOME)