def velcal(lc, posa, potim, num=None, bound=0.1):
#????????????????,?????????(??????2~n-1??)
import numpy as np
import vasp
if num == None:
timestep = 2 * potim
vela = [0] * (len(posa) - 2)
check = False
for i in range(len(vela)):
vela[i] = np.mat(np.zeros((len(posa[1]), 3)))
for i in range(len(posa) - 2):
# print(i) #??
for j in range(len(posa[1])):
for k in range(3):
# if abs(posa[i+2][j,k]) < 0.05 or abs(posa[i+2][j,k]-1) < 0.05 or abs(posa[i+2][j,k]) or abs(posa[i][j,k])> 1: #????
if abs(posa[i + 2][j,
k]) < bound or abs(posa[i + 2][j, k] -
1) < bound: #????
check = True
break
if check:
posa[i + 2][j, :] = vasp.nearby(lc, posa[i][j, :],
posa[i + 2][j, :])
check = False
vela[i][j, :] = (posa[i + 2][j, :] -
posa[i][j, :]) * lc / timestep
return vela
else:
num -= 1
timestep = 2 * potim
vela = [0] * (len(posa) - 2)
check = False
for i in range(len(vela)):
vela[i] = np.mat(np.zeros((1, 3)))
for i in range(len(vela)):
# print(i) #??
for k in range(3):
# if abs(posa[i+2][num,k]) < 0.05 or abs(posa[i+2][num,k]-1) < 0.05 or abs(posa[i+2][num,k]) > 1 or abs(posa[i][num,k]) > 1: #????
if abs(posa[i + 2][num,
k]) < bound or abs(posa[i + 2][num, k] -
1) < bound: #????
check = True
break
if check:
posa[i + 2][num, :] = vasp.nearby(lc, posa[i][num, :],
posa[i + 2][num, :])
check = False
vela[i][:] = (posa[i + 2][num, :] -
posa[i][num, :]) * lc / timestep
return vela
def bond_angle(ap, lc, arg1, arg2, arg3):
#????????
import numpy as np
import vasp
import math
arg1 -= 1
arg2 -= 1
arg3 -= 1
ap[arg1, :] = vasp.nearby(lc, ap[arg2, :], ap[arg1, :])
ap[arg3, :] = vasp.nearby(lc, ap[arg2, :], ap[arg3, :])
dp1 = ap[arg1, :] * lc
dp2 = ap[arg2, :] * lc
dp3 = ap[arg3, :] * lc
ll1 = dp2 - dp1
ll2 = dp2 - dp3
cita = math.acos(ll1 * np.transpose(ll2) / math.sqrt(
(ll1 * np.transpose(ll1)) * (ll2 * np.transpose(ll2)))) * 180 / math.pi
return cita
def checkaway(lc,
posa,
vela,
num,
oneatom=True,
dis_lim=5,
v_d_lim=0.10): #????
#???????????
import numpy as np
import math
import vasp
num -= 1
nstep = len(posa)
check = False
if oneatom:
for n in range(7):
step = int((n + 1) * nstep / 8)
posa[step][num, :] = vasp.nearby(lc, posa[0][num, :],
posa[step][num, :])
dp = (posa[step][num, :] - posa[0][num, :]) * lc
dis = math.sqrt(dp * np.transpose(dp))
disv = dp * np.transpose(vela[step])
if dis > dis_lim:
check = True
break
elif disv > v_d_lim:
check = True
break
return check
else:
for n in range(7):
step = int((n + 1) * nstep / 8)
posa[step][num, :] = vasp.nearby(lc, posa[0][num, :],
posa[step][num, :])
dp = (posa[step][num, :] - posa[0][num, :]) * lc
dis = math.sqrt(dp * np.transpose(dp))
disv = dp * np.transpose(vela[step][num, :])
if dis > dis_lim:
check = True
break
elif disv > v_d_lim:
check = True
break
return check
def bond_length(ap, lc, arg1, arg2):
#????????
import numpy as np
import vasp
import math
arg1 -= 1
arg2 -= 1
ap[arg2, :] = vasp.nearby(lc, ap[arg1, :], ap[arg2, :])
dp1 = ap[arg1, :] * lc
dp2 = ap[arg2, :] * lc
dis = (dp1 - dp2) * np.transpose(dp1 - dp2)
dis = math.sqrt(dis)
return dis