def cp():
p,zpe,spec,bonds,offd,angs,torp,hbs= read_lib(libfile='ffield')
p_ = p.copy()
p_chon,zpe,spec,bonds,offd,angs,torp,hbs= read_lib(libfile='ffieldCHON')
for key in p_chon:
if not key in p_:
# print(key)
p_[key] = p_chon[key]
write_lib(p_,spec,bonds,offd,angs,torp,hbs,libfile='ffield_')
def i():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
fj = open('ffield.json', 'w')
j = {'p': p, 'm': [], 'bo_layer': [], 'zpe': []}
js.dump(j, fj, sort_keys=True, indent=2)
fj.close()
def plro(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.arange(0.0001, 3.0, 0.1)
ro = np.arange(0.75, 1.85, 0.15)
plt.figure()
plt.ylabel('Uncorrected ' + lab + 'Bond Order')
plt.xlabel(r'$Radius$ $(Angstrom)$')
plt.xlim(0, 3.0)
plt.ylim(0, 1.01)
bd = 'C-H'
# for i,bd in enumerate(bonds):
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
for i, rosi in enumerate(ro):
b = get_bo(r, rosi=rosi, bo1=p['bo1_' + bd], bo2=p['bo2_' + bd])
plt.plot(r,
b,
label=r'$r_{sigma}=%f$' % rosi,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
plt.legend()
plt.savefig('bovsro.eps')
plt.close()
def plbo3d(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.linspace(0.0001, 3.0, 50)
bo2_ = np.linspace(0.001, 18.0, 50)
bo1_ = np.linspace(-0.9, -0.0001, 50)
bo1_, bo2_ = np.meshgrid(bo1_, bo2_)
bd = 'C-C'
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
b = get_bo(r, rosi=p['rosi_' + bdn], bo1=bo1_, bo2=bo2_)
fig = plt.figure()
ax = Axes3D(fig)
# plt.xlabel("Delta'")
ax = plt.subplot(111, projection='3d')
ax.plot_surface(bo1_, bo2_, b, cmap=plt.get_cmap('rainbow'))
ax.contourf(bo1_,
bo2_,
b,
zdir='z',
offset=0.0,
cmap=plt.get_cmap('rainbow'))
plt.savefig('bovsbo23d.eps')
plt.close()
def q(gen='packed.gen'):
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
A = read(gen)
q = qeq(p=p, atoms=A)
q.calc(A)
# q.debug()
print('\n- Qeq Charges: \n', q.q[:-1])
def cpl():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(
libfile='ffield-FromPaperSort')
p_ = {}
specs = ['Al', 'C', 'H']
for key in p:
k = key.split('_')
if len(k) == 1:
p_[key] = p[key]
else:
bd = k[1]
b = bd.split('-')
if len(b) == 1:
if b[0] in specs:
if b[0] == 'H':
p_[k[0] + '_' + 'F'] = p[key]
else:
p_[key] = p[key]
elif len(b) == 2:
if b[0] in specs and b[1] in specs:
if b[0] == 'H' or b[1] == 'H':
bd_ = bd.replace('H', 'F')
p_[k[0] + '_' + bd_] = p[key]
else:
p_[key] = p[key]
elif len(b) == 3:
if b[0] in specs and b[1] in specs and b[2] in specs:
if b[0] == 'H' or b[1] == 'H' or b[2] == 'H':
bd_ = bd.replace('H', 'F')
p_[k[0] + '_' + bd_] = p[key]
else:
p_[key] = p[key]
elif len(b) == 4:
if b[0] in specs and b[1] in specs and b[2] in specs and b[
3] in specs:
if b[0] == 'H' or b[1] == 'H' or b[2] == 'H' or b[3] == 'H':
bd_ = bd.replace('H', 'F')
p_[k[0] + '_' + bd_] = p[key]
else:
p_[key] = p[key]
spec_ = ['C', 'F', 'Al']
# write_lib(p_,spec_,bonds,offd,angs,torp,hbs,libfile='ffield_')
with open('ffield.json', 'w') as fj:
j = {
'p': p_,
'm': None,
'EnergyFunction': 0,
'MessageFunction': 0,
'messages': 1,
'bo_layer': None,
'bf_layer': None,
'be_layer': None,
'vdw_layer': None,
'MolEnergy': None
}
js.dump(j, fj, sort_keys=True, indent=2)
def get_p(ffield):
if ffield.endswith('.json'):
lf = open(ffield, 'r')
j = js.load(lf)
p = j['p']
m = j['m']
spec, bonds, offd, angs, torp, hbs = init_bonds(p)
else:
p, zpe_, spec, bonds, offd, Angs, torp, Hbs = read_lib(libfile=ffield,
zpe=False)
return p, bonds
def jj():
lf = open('ffield.json', 'r')
j = js.load(lf)
p_ = j['p']
m_ = j['m']
bo_layer_ = j['bo_layer']
lf.close()
spec, bonds, offd, angs, torp, hbs = init_bonds(p_)
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
fj = open('ffield_.json', 'w')
j = {'p': p, 'm': m_, 'bo_layer': bo_layer}
js.dump(j, fj, sort_keys=True, indent=2)
fj.close()
def resetff():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(
libfile='ffield.reax')
# print(torp)
p_ = p.copy()
Poffd = ['Devdw', 'rvdw', 'alfa', 'rosi', 'ropi', 'ropp']
for bd in bonds:
b = bd.split('-')
if b[0] != b[1]:
if bd not in offd:
# print(bd)
offd.append(bd)
for ofd in Poffd:
if p_[ofd + '_' + b[0]] > 0 and p_[ofd + '_' + b[1]] > 0:
p_[ofd + '_' + bd] = np.sqrt(p_[ofd + '_' + b[0]] *
p_[ofd + '_' + b[1]])
else:
p_[ofd + '_' + bd] = -1.0
for key in p:
k = key.split('_')
kpre = k[0]
if kpre == 'ropi' or kpre == 'ropp':
pcon = k[1]
pc_ = pcon.split('-')
if p[key] <= 0.0:
if pcon != 'X':
if len(pc_) == 2:
p_['bo3_' + pcon] = -50.0
p_['bo4_' + pcon] = 2.0
else:
p_['bo3_' + pcon + '-' + pcon] = -50.0
p_['bo4_' + pcon + '-' + pcon] = 2.0
for key in p:
k = key.split('_')
kpre = k[0]
if kpre == 'ropi' or kpre == 'ropp':
pcon = k[1]
if kpre == 'ropi':
p_[key] = 0.9 * p['rosi_' + pcon]
elif kpre == 'ropp':
p_[key] = 0.8 * p['rosi_' + pcon]
p_, tors = check_tors(p_, spec, torp)
write_lib(p_, spec, bonds, offd, angs, tors, hbs, libfile='ffield')
def plbo1(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.arange(0.0001, 3.0, 0.1)
bo1_ = np.arange(-2.0, -0.0001, 0.05)
plt.figure()
plt.ylabel('Uncorrected ' + lab + 'Bond Order')
plt.xlabel(r'$Radius$ $(Angstrom)$')
plt.xlim(0, 2.6)
plt.ylim(0, 1.01)
bd = 'C-C'
# for i,bd in enumerate(bonds):
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
for i, bo1 in enumerate(bo1_):
b = get_bo(r, rosi=p['rosi_' + bdn], bo1=bo1, bo2=p['bo2_' + bd])
if i == 0:
plt.plot(r,
b,
label=r'$bo1=%f$' % bo1,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
elif i == len(bo1_) - 1:
plt.plot(r,
b,
label=r'$bo1=%f$' % bo1,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
else:
plt.plot(
r,
b, # label=r'$bo1=%f$' %bo1,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
plt.legend()
plt.savefig('bovsbo1.eps')
plt.close()
def i():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
fj = open('ffield.json', 'w')
# j = {'p':p,'m':[],'bo_layer':[],'zpe':[]}
j = {
'p': p,
'm': None,
'EnergyFunction': 0,
'MessageFunction': 0,
'messages': 1,
'bo_layer': None,
'bf_layer': None,
'be_layer': None,
'vdw_layer': None,
'MolEnergy': None
}
js.dump(j, fj, sort_keys=True, indent=2)
fj.close()
def ii():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
write_lib(p_, spec, bonds, offd, angs, torp, hbs, libfile='ffield_')
def q(gen='packed.gen'):
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
A = read(gen)
q = qeq(p=p, atoms=A)
q.calc()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib
matplotlib.use('Agg')
from os import system, getcwd, chdir, listdir
from os.path import isfile # exists
import argh
import argparse
from irff.reax import ReaxFF
from irff.mpnn import MPNN
from irff.reaxfflib import read_lib, write_lib
direcs = {'alc2f6': '/home/feng/mlff/Al/alc2f6'} # can by multi-directories
batch = 50 # number of frame need to collected from directories.
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
vto = [] ## define variables to optimize
for key in p:
k = key.split('_')
if len(k) == 1:
continue
kpre = k[0]
kc = k[1]
kc_ = kc.split('-')
if kpre == 'n.u.':
continue
# if kpre=='Devdw':
# continue
