def VaspNEBCheckRMS():
print('CheckNEBRMS is running...')
if '00' in os.listdir() and 'INCAR' in os.listdir():
data_INCAR = zzd.File.openFile('./INCAR')
data_log = zzd.File.openFile('./log')
image = zzd.File.getLine(data_INCAR,
'IMAGES')[0].split('=')[-1].strip('\n')
#print(zzd.File.getAllline(data_log,'F='))
ionstep = zzd.File.getAllline(data_log, 'F=')[-1].split()[0]
if int(image) <= 9:
#print('aa')
#data00 = zzd.getshellResult('grep RMS 00/OUTCAR')
data01 = zzd.getshellResult('grep RMS 01/OUTCAR')
data02 = zzd.getshellResult('grep RMS 02/OUTCAR')
data03 = zzd.getshellResult('grep RMS 03/OUTCAR')
#data04 = zzd.getshellResult('grep RMS 04/OUTCAR')
#print(data00)
print('{:^3}{:^10}{:^10}{:^10}{:^10}'.format(
'Step', '01-RMS', '02-RMS', '03-RMS', '01+02+03'))
for i in range(int(ionstep)):
print('{:>3}{:>10}{:>10}{:>10}{:>10.6f}'.format(
i + 1, data01[i].split()[4], data02[i].split()[4],
data03[i].split()[4],
float(data01[i].split()[4]) + float(data02[i].split()[4]) +
float(data03[i].split()[4])))
else:
print('不在NEB目录，退出程序')
exit()
def VaspNEBCheckDist(POSorCONT):
if '00' in os.listdir() and 'INCAR' in os.listdir():
data_log = zzd.File.openFile('./INCAR')
image = zzd.File.getLine(data_log,
'IMAGES')[0].split('=')[-1].strip('\n')
if int(image) <= 9:
#os.system('cp ini/CONTCAR 00/CONTCAR')
#os.system('cp fin/CONTCAR 0'+str(int(image)+1)+'/CONTCAR')
for i in range(0, int(image) + 1):
if i == 0:
dist = zzd.getshellResult('dist.pl ./0' + str(i) +
'/POSCAR ./0' + str(i + 1) +
'/' + POSorCONT)
elif i == int(image):
dist = zzd.getshellResult('dist.pl ./0' + str(i) + '/' +
POSorCONT + ' ./0' + str(i + 1) +
'/POSCAR')
else:
dist = zzd.getshellResult('dist.pl ./0' + str(i) + '/' +
POSorCONT + ' ./0' + str(i + 1) +
'/' + POSorCONT)
print('{} 0{}-0{} {}'.format(POSorCONT, i, i + 1,
dist[0].strip('\n')))
else:
print('image too large')
else:
print('当前不在NEB目录，退出程序')
exit()
def run2(ele):
atoms = [53, 16, 12, 25, 14, 17, 23, 26, 39, 40, 37, 42, 31, 48, 27, 36, 30, 28, 13, 11, 5]
fre1 = np.array([])
for i in range(len(atoms)):
atom = str(atoms[i])
code = f'grep THz {ele}-Energies/{ele}-V/52Fe1{ele}1V/vib_analysis/atom{atom}/OUTCAR'
result = zzdlib.getshellResult(code)
fre = decode_vib_frequency(result)
fre1 = np.concatenate((fre1, fre), axis=0)
print(fre1.shape)
vac_1nn = np.array([6.6160, 6.6107, 5.5804])
vac_2nn = np.array([7.0517, 7.0461, 6.6759])
item1 = np.power(np.prod(vac_1nn), 8) * np.power(np.prod(vac_2nn), 6)
pure = np.array([7.0748, 7.0727, 7.0708])
item2 = np.power(np.prod(pure), 8)
sol = np.array([6.4545, 6.4515, 6.4482])
sol_1nn = np.array([7.0020, 6.9931, 6.8190])
sol_2nn = np.array([7.1250, 7.0793, 7.0716])
item3 = np.prod(sol) * np.power(np.prod(sol_1nn), 8) * np.power(np.prod(sol_2nn), 6)
item4 = np.prod(fre1)
inner = item1 * item3 / item2 / item4
Sb = np.log(inner)
print(f'item1: {item1}\nitem2: {item2} \nitem3: {item3} \nitem4: {item4}\n inner: {inner} Sb: {Sb}')
def get_Hm_and_v_from_raw():
cases = 'w0_3nn,w1,w2,w3_2nn,w3_3nn,w3_4nn'.split(',')
Hm_list = []
v_list = []
for i in range(len(cases)):
case = cases[i]
os.chdir(case)
# 获取Hm
# print(pys_path, os.getcwd())
res = zzdlib.getshellResult(f'python3 {pys_path}/NEBCheck.py --func=2')
# print(res)
line, index = zzdlib.File.getLine(res, 'IMAGE')
IMAGE = []
Barrier = []
# print(res)
for j in range(index + 1, len(res)):
if res[j] == '\n':
break
img = int(res[j].split()[0])
barrier = float(res[j].split()[-1])
IMAGE.append(img)
Barrier.append(barrier)
Hm_foreward = np.max(Barrier)
Hm_backward = np.max(Barrier) - Barrier[-1]
Hm_list.append(Hm_foreward)
Hm_list.append(Hm_backward)
# 获取v
code = f'python3 {pys_path}/VaspVibAna_Result.py --isprint=True'
res = zzdlib.getshellResult(code)
v_foreward = zzdlib.File.getLine(res,
keywords='foreward')[0].split()[-1]
v_backward = zzdlib.File.getLine(res,
keywords='backward')[0].split()[-1]
if v_backward == 'Match':
v_backward = '0'
v_list.append(float(v_foreward))
v_list.append(float(v_backward))
os.chdir('..')
def run(ele, correct=False):
code1 = f'grep THz {ele}-Energies/{ele}-V/52Fe1{ele}1V/vib_analysis/*/OUTCAR'
result1 = zzdlib.getshellResult(code1)
fre1 = decode_vib_frequency(result1)
code2 = f'grep THz {ele}-Energies/{ele}-V/53Fe1{ele}/vib_analysis/*/OUTCAR'
result2 = zzdlib.getshellResult(code2)
fre2 = decode_vib_frequency(result2)
print(fre1.shape, fre2.shape)
# 主要是因为bcc_withCr 中 52Fe1Cr1V的atom46原子振动计算没有完成，fre1缺少一个原子的振动数据，用其他的原子的振动的平均值补充上去
if correct:
number = fre1.shape[0]
row = int(number/3)
print(f'总{number} 行{row}')
fre1 = fre1.reshape(row, 3)
fre1_mean = np.mean(fre1, axis=0)
fre1_mean = fre1_mean.reshape(1, 3)
fre1 = np.concatenate((fre1, fre1_mean), axis=0)
fre1 = fre1.reshape(number+3)
vac_1nn = np.array([6.6160, 6.6107, 5.5804])
vac_2nn = np.array([7.0517, 7.0461, 6.6759])
item1 = np.power(np.prod(vac_1nn), 8) * np.power(np.prod(vac_2nn), 6)
pure = np.array([7.0748, 7.0727, 7.0708])
item2 = np.power(np.prod(pure), 15)
item4 = np.prod(fre1)
item3 = np.prod(fre2)
inner = item1 * item3 / item2 / item4
Sb = np.log(inner)
print(f'item1: {item1}\nitem2: {item2} \nitem3: {item3} \nitem4: {item4}\n inner: {inner} Sb: {Sb}')
def grep_fre(path):
code = f'grep THz {path}/OUTCAR'
result = zzdlib.getshellResult(code)
fre = decode_vib_frequency(result)
return fre
def getBarrier(IS='-1'):
#IS代表输入的Ionstep，根据IS获取该步时候的扩散势垒
Path = []
Barrier = []
Step = []
Image = []
runpath = os.getcwd()
for dirpath, dirnames, filenames in os.walk('./'):
if 'INCAR' in filenames and 'POTCAR' in filenames and 'KPOINTS' in filenames:
data_INCAR = zzd.File.openFile(dirpath + '/INCAR', 'r')
#print('dir',data_INCAR[0].split('=')[-1])
if 'NEB' in data_INCAR[0].split('=')[-1]:
#print('NEB')
data_Sh = zzd.File.openFile(dirpath + '/Vasp.sh', 'r')
jobname = zzd.File.getLine(
data_Sh, '#PBS -N')[0].split()[-1][:10] #获取任务名，且只取前10个字符
stat = zzd.Vasp.checkJobstatus(jobname)
if stat == 'R' or stat == 'Q':
print('路径{} NEB计算正在{}'.format(dirpath, stat))
elif 'log' in os.listdir(dirpath): #未提交或者已经算完：
data_log = zzd.File.openFile(dirpath + '/log', 'r')
isRA = zzd.File.getLine(data_log,
'reached required accuracy')[0]
images = zzd.File.getLine(data_INCAR,
'IMAGES')[0].split('=')[-1]
Fstep = zzd.File.getLine(data_INCAR,
'NSW')[0].split('=')[-1]
ionstep = zzd.File.getAllline(data_log,
'F=')[-1].split()[0]
if 'reached required accuracy' in isRA or Fstep == ionstep:
#print('RA')
barriers = []
os.chdir(dirpath)
if IS == '-1': #默认用nebef.pl获取势垒
nebef = zzd.getshellResult('nebef.pl')
for inn in nebef:
barriers.append(float(inn.split()[3]))
else: #获取输出的步数IS，计算该步数下的势垒。
try:
data_OUTini = zzd.File.openFile(
'./00/OUTCAR', 'r')
Eini = zzd.File.getAllline(
data_OUTini,
'energy without entropy')[-1].split()[-1]
data_OUTfin = zzd.File.openFile(
'./0' + str(int(images) + 1) + '/OUTCAR',
'r')
Efin = zzd.File.getAllline(
data_OUTini,
'energy without entropy')[-1].split()[-1]
barriers.append(float(Eini) - float(Eini))
for ii in range(1, int(images) + 1):
data = zzd.File.openFile(
'./0' + str(ii) + '/stdout', 'r')
Ener = zzd.File.getLine(
data, IS + ' F=')[0].split()[4]
barriers.append(float(Ener) - float(Eini))
except Exception as e:
print('获取第{}步势垒出现问题，提示为：{}'.format(IS, e))
Barrier.append(max(barriers))
Step.append(ionstep)
Path.append(dirpath[:18])
Image.append(images)
os.chdir(runpath)
else:
print('{} 未达到收敛标准或者计算步数未满，退出'.format(dirpath))
else:
print('出现了奇怪的问题')
print('{:<20}{:<10}{:<5}{:<3}'.format('path', 'barrier', 'step', 'images'))
for i in range(len(Barrier)):
print('{:<20}{:<10.7f}{:<5}{:<3}'.format(Path[i], Barrier[i], Step[i],
Image[i]))
def CheckWARNING(usript):
#usrinput为1时，只打印是否完成，为2时候，只打印能量信息，为3时，打印全部
Path = []
Energy = []
Step = []
mag = []
dist = []
RMS = []
warnflag = 0
jstat = ['Running...', 'Done', 'SC Running...', 'SC done', 'Stoped']
for dirpath, dirnames, filenames in os.walk('./'):
if 'INCAR' in filenames and 'POSCAR' in filenames and 'Vasp.sh' in filenames:
data_Sh = zzd.File.openFile(dirpath + '/Vasp.sh', 'r')
data_INCAR = zzd.File.openFile(dirpath + '/INCAR', 'r')
SYSTEM = zzd.File.getLine(data_INCAR, 'SYSTEM')[0].split('=')[-1]
jobname = zzd.File.getLine(data_Sh,
'#PBS -N')[0].strip('\n').split()[-1]
jobstatus = zzd.Vasp.checkJobstatus(jobname)
#print('Path:{} {} {}'.format(dirpath,jobstatus,jobname))
if jobstatus == 'Q':
print('Path:{:<60}任务正在排队... '.format(dirpath))
elif jobstatus == 'R' or 'log' in filenames: #正在计算和算完了用相同的检测方法
if usript == '1' or usript == '3':
data_log = zzd.File.openFile(dirpath + '/log', 'r')
reachRA = zzd.File.getLine(data_log,
'reached required accuracy')[0]
try:
RMM = zzd.File.getAllline(data_log,
'RMM:')[-1].split()[1]
RMM = RMM + ' RMM'
except:
RMM = '0 RMM'
try:
DAV = zzd.File.getAllline(data_log,
'DAV:')[-1].split()[1]
DAV = DAV + ' DAV'
except:
DAV = '0 DAV'
termination = zzd.File.getLine(
data_log, 'Ctrl-C caught... cleaning up processes')[0]
try:
ionstep = zzd.File.getAllline(data_log,
'F=')[-1].split()[0]
except:
ionstep = '0'
#print('Path:{} {} {}'.format(dirpath,reachRA,v1F))
if 'reached required accuracy' in reachRA:
print('Path:{:<60}{:<15}{:>3}F{:>9}'.format(
dirpath, jstat[1], ionstep, RMM))
elif SYSTEM == 'Self' or SYSTEM == 'Static' or SYSTEM == 'self' or SYSTEM == 'static':
vRMM = zzd.File.getLine(data_log, 'RMM:')[0]
vDAV = zzd.File.getLine(data_log, 'DAV:')[0]
if ('DAV:' in vDAV
or 'RMM:' in vRMM) and ionstep == '0':
print('Path:{:<60}{:<15}{:>3}F{:>9}{:>7}{:>5}'.
format(dirpath, jstat[2], ionstep, RMM, DAV,
'*'))
elif ionstep == '1': #没有完成，但有1F了
print('Path:{:<60}{:<15}{:>3}F{:>9}'.format(
dirpath, jstat[3], ionstep, RMM))
elif 'cleaning up processes' in termination:
print('Path:{:<60}{:<15}{:>3}F{:>9}{:>7}'.format(
dirpath, jstat[4], ionstep, RMM, DAV))
else:
print('Path:{:<60}{:<15}{:>3}F{:>9}{:>7}{:>5}'.format(
dirpath, jstat[0], ionstep, RMM, DAV, '*'))
# 检查警告
try:
data_OUTCAR = zzd.File.openFile(
dirpath + '/OUTCAR', 'r')
WARNING_log = zzd.File.getAllline(data_log, 'WARNING')
WARNING_OUT = zzd.File.getAllline(
data_OUTCAR, 'WARNING')
ERROR_log = zzd.File.getAllline(data_log, 'ERROR')
if WARNING_log != [] or WARNING_OUT != []:
print('Path:{:<60} 出现警告'.format(
dirpath, ionstep))
zzd.File.printData(WARNING_log)
zzd.File.printData(WARNING_OUT)
warnflag = 1
if ERROR_log != []:
zzd.File.printData(ERROR_log)
warnflag = 1
except Exception as e:
print('path:{} {}'.format(dirpath, e))
if usript == '2' or usript == '3':
#打印能量信息
data_log = zzd.File.openFile(dirpath + '/log', 'r')
try:
log_lastF = zzd.File.getAllline(data_log, 'F=')[-1]
except:
log_lastF = '0 F= 0 E0= 0 d E 0 mag= 0' #在存在log，Log中连1步都没算完的时候
if len(dirpath) > 15:
path = '...' + dirpath[-15:]
else:
path = dirpath
Path.append(path)
Energy.append(log_lastF.split()[4])
Step.append(log_lastF.split()[0])
try:
mag.append(log_lastF.split()[9])
except:
mag.append('0')
dist.append(
zzd.getshellResult('dist.pl ' + dirpath + '/POSCAR ' +
dirpath +
'/CONTCAR')[-1].strip('\n'))
try:
RMS.append(
zzd.getshellResult('grep RMS ' + dirpath +
'/OUTCAR')[-1].split()[4])
except: #如果出现没算完，grep返回一个空的列表的时候
RMS.append('0')
if (usript == '1' or usript == '3') and warnflag == 0:
print('无警告或错误')
if (usript == '2' or usript == '3'):
print('{:<18}{:<11}{:<5}{:^10}{:^10}{:^10}'.format(
'路径', '能量', '步数', 'mag', 'dist', 'RMS'))
for i in range(len(Path)):
print('{:<20}{:<13.4f}{:<7}{:<12.4f}{:<10.4f}{:<10.4f}'.format(
Path[i], eval(Energy[i]), Step[i], eval(mag[i]), eval(dist[i]),
eval(RMS[i])))