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add stretch-bend cross term

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This commit is contained in:
Steve Plimpton
2021-12-15 16:34:28 -07:00
parent 67f7e44688
commit c479d78854
5 changed files with 4682 additions and 3847 deletions
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8364
examples/amoeba/data.ubiquitin
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1
examples/amoeba/in.ubiquitin
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@ -8,6 +8,7 @@ atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO

12
src/AMOEBA/angle_amoeba.cpp
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@ -169,8 +169,9 @@ void AngleAmoeba::compute(int eflag, int vflag)
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
//if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
// k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
eangle = 0.0;
// force & energy for bond-angle term
// bond-stretch cross term in Tinker
@ -216,6 +217,9 @@ void AngleAmoeba::compute(int eflag, int vflag)
if (eflag) eangle += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
printf("Stretch-Bend: %ld %d %d: eng %g\n",
atom->tag[i1],atom->tag[i2],atom->tag[i3],eangle);
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
@ -445,6 +449,9 @@ void AngleAmoeba::allocate()
memory->create(ba_r2,n+1,"angle:ba_r2");
memory->create(setflag,n+1,"angle:setflag");
memory->create(setflag_a,n+1,"angle:setflag");
memory->create(setflag_ba,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = setflag_a[i] = setflag_ba[i] = 0;
}
@ -500,6 +507,7 @@ void AngleAmoeba::coeff(int narg, char **arg)
k4[i] = k4_one;
k5[i] = k5_one;
k6[i] = k6_one;
setflag_a[i] = 1;
count++;
}
}

7
src/AMOEBA/improper_amoeba.cpp
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@ -272,16 +272,12 @@ void ImproperAmoeba::init_style()
Pair *pair = force->pair_match("amoeba",1,0);
if (!pair) pair = force->pair_match("hippo",1,0);
if (!pair) error->all(FLERR,"Improper amoeba could not find pair amoega");
int dim;
opbend_cubic = *(double *) pair->extract("opbend_cubic",dim);
opbend_quartic = *(double *) pair->extract("opbend_quartic",dim);
opbend_pentic = *(double *) pair->extract("opbend_pentic",dim);
opbend_sextic = *(double *) pair->extract("opbend_sextic",dim);
printf("OPBEND %g %g %g %g\n",
opbend_cubic,opbend_quartic,opbend_pentic,opbend_sextic);
}
/* ----------------------------------------------------------------------
@ -301,9 +297,8 @@ void ImproperAmoeba::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
if (comm->me == 0)
utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,nullptr,error);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;

145
tools/tinker2lmp.py
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@ -36,7 +36,7 @@ def error(txt=""):
print " -nopbc"
print " -pbc xhi yhi zhi"
else: print "ERROR:",txt
sys.exit()
#sys.exit()
# read and store values from a Tinker xyz file
@ -251,13 +251,13 @@ class PRMfile:
def bondangles(self):
params = []
iline = self.find_section("Stretch Bend Parameters")
iline = self.find_section("Stretch-Bend Parameters")
if iline < 0: return params
iline += 3
bdict = {}
for m,params in enumerate(self.bondparams):
bdict[(params[0],params[1])] = params[2]
for m,bparams in enumerate(self.bondparams):
bdict[(bparams[0],bparams[1])] = bparams[2]
while iline < self.nlines:
words = self.lines[iline].split()
@ -271,14 +271,27 @@ class PRMfile:
value2 = float(words[5])
lmp1 = value1
lmp2 = value2
lmp3 = lmp4 = 0.0
if (class2,class1) in bdict: lmp3 = bdict[(class2,class1)]
if (class1,class2) in bdict: lmp3 = bdict[(class1,class2)]
if (class2,class3) in bdict: lmp4 = bdict[(class2,class3)]
if (class3,class2) in bdict: lmp4 = bdict[(class3,class2)]
if lmp3 == 0.0 or lmp4 == 0.0:
print "Bond in BondAngle term not found",class1,class2,class3
sys.exit()
if (class1,class2) in bdict:
lmp3 = bdict[(class1,class2)]
elif (class2,class1) in bdict:
lmp3 = bdict[(class2,class1)]
else:
error("1st bond in BondAngle term not found: %d %d %d" % \
(class1,class2,class3))
# NOTE: just for debugging
lmp3 = 0.0
if (class2,class3) in bdict:
lmp4 = bdict[(class2,class3)]
elif (class3,class2) in bdict:
lmp4 = bdict[(class3,class2)]
else:
error("2nd bond in BondAngle term not found: %d %d %d" % \
(class1,class2,class3))
# NOTE: just for debugging
lmp4 = 0.0
params.append((class1,class2,class3,lmp1,lmp2,lmp3,lmp4))
iline += 1
return params
@ -301,12 +314,11 @@ class PRMfile:
class4 = int(words[4])
if len(words) <= 5:
print "Torsion has no params",class1,class2,class3,class4
sys.exit()
error("Torsion has no params: %d %d %d %d" % \
(class1,class2,class3,class4))
if (len(words)-5) % 3:
print "Torsion does not have triplets of params", \
class1,class2,class3,class4
sys.exit()
error("Torsion does not have triplets of params: %d %d %d %d" % \
(class1,class2,class3,class4))
mfourier = (len(words)-5) / 3
oneparams = [class1,class2,class3,class4,mfourier]
@ -603,9 +615,7 @@ for atom1,atom2 in blist:
if (c1,c2) in bdict: m,params = bdict[(c1,c2)]
elif (c2,c1) in bdict: m,params = bdict[(c2,c1)]
else:
print "Bond not found",atom1,atom2,c1,c2
sys.exit()
else: error("Bond not found: %d %d: %d %d" % (atom1,atom2,c1,c2))
if not flags[m]:
v1,v2,v3,v4 = params[2:]
@ -615,7 +625,6 @@ for atom1,atom2 in blist:
# generate atype = LAMMPS type of each angle
# generate aparams = LAMMPS params for each angle type
# generate baparams = LAMMPS bond-angle params for each angle type
# flags[i] = which LAMMPS angle type (1-N) the Tinker FF file angle I is
# 0 = none
# Tinker FF file angle entries can have 1, 2, or 3 options
@ -636,12 +645,11 @@ for m,params in enumerate(prm.angleparams):
noptions += n
flags = noptions*[0]
#baflags = len(baprm)*[0]
atype = []
aparams = []
baparams = []
for atom1,atom2,atom3 in alist:
for i,one in enumerate(alist):
atom1,atom2,atom3 = one
type1 = type[atom1-1]
type2 = type[atom2-1]
type3 = type[atom3-1]
@ -651,8 +659,19 @@ for atom1,atom2,atom3 in alist:
if (c1,c2,c3) in adict or (c3,c2,c1) in adict:
if (c1,c2,c3) in adict: m,params = adict[(c1,c2,c3)]
if (c3,c2,c1) in adict: m,params = adict[(c3,c2,c1)]
# IMPORTANT subtlety
# flip order of 3 atoms in alist if the angle
# matches Angle Bending section of PRM file in reverse order
# necessary b/c BondAngle coeffs will be generated with r1,r2 params
# from Bond Stretching section of PRM file
# since in general r1 != r2, the LAMMPS AngleAmoeba class requires
# the 3 atoms in the angle be in the order that matches r1 and r2
if (c3,c2,c1) in adict:
m,params = adict[(c3,c2,c1)]
alist[i] = (atom3,atom2,atom1)
# params is a sequence of 1 or 2 or 3 options
# which = which of 1,2,3 options this atom triplet matches
# for which = 2 or 3, increment m to index correct position in flags
@ -679,7 +698,7 @@ for atom1,atom2,atom3 in alist:
print " angle atom classes:",c1,c2,c3
print " Tinker FF file param options:",len(params[3])
print " Nbonds and hydrogen count:",nbonds,hcount
#sys.exit() // NOTE: allow this for now
#sys.exit() NOTE: allow this for now
if hcount == 0: which = 1
elif hcount == 1:
@ -702,7 +721,7 @@ for atom1,atom2,atom3 in alist:
print " angle atom classes:",c1,c2,c3
print " Tinker FF file param options:",len(params[3])
print " Nbonds and hydrogen count:",nbonds,hcount
#sys.exit() // NOTE: allow this for now
#sys.exit() NOTE: allow this for now
if hcount == 0: which = 1
elif hcount == 1:
@ -713,8 +732,7 @@ for atom1,atom2,atom3 in alist:
m += 2
else:
print "Angle not found",atom1,atom2,atom3,c1,c2,c3
sys.exit()
error("Angle not found: %d %d %d: %d %d %d" % (atom1,atom2,atom3,c1,c2,c3))
if not flags[m]:
pflag,v1,v2,v3,v4,v5,v6 = params[3][which-1]
@ -722,24 +740,36 @@ for atom1,atom2,atom3 in alist:
flags[m] = len(aparams)
atype.append(flags[m])
# NOTE: baparams may need to be flipped if match is 3,2,1 instead of 1,2,3
# NOTE: mismatch between angle and bondangle params may not be handled right
# should be a new LAMMPS type if either angle or bondangle params do not match?
#for m,params in enumerate(baprm):
# c1,c2,c3,v1,v2,v3,v4 = params
# if (c1 == class1 and c2 == class2 and c3 == class3) or \
# (c1 == class3 and c2 == class2 and c3 == class1):
# found += 1
# if baflags[m]:
# continue
# #atype.append(baflags[m])
# else:
# baparams.append((v1,v2,v3,v4))
# baflags[m] = len(baparams)
# #atype.append(baflags[m])
# break
# if found != 1: print "Not found",atom1,atom2,atom3,class1,class2,class3
# augment the aparams with bond-angle cross terms from bondangleparams
# generate baparams = LAMMPS bond-angle params for each angle type
# sbdict = dictionary for angle tuples in bongangleparams
sbdict = {}
for v1,v2,v3,v4,v5,v6,v7 in prm.bondangleparams:
if (v1,v2,v3) in sbdict: continue
sbdict[(v1,v2,v3)] = (v4,v5,v6,v7)
baparams = []
for itype in range(len(aparams)):
iangle = atype.index(itype+1)
atom1,atom2,atom3 = alist[iangle]
type1 = type[atom1-1]
type2 = type[atom2-1]
type3 = type[atom3-1]
c1 = classes[type1-1]
c2 = classes[type2-1]
c3 = classes[type3-1]
if (c1,c2,c3) in sbdict:
n1,n2,r1,r2 = sbdict[(c1,c2,c3)]
elif (c3,c2,c1) in sbdict:
n1,n2,r1,r2 = sbdict[(c3,c2,c1)]
else:
print "Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3)
n1,n2,r1,r2 = 4*[0.0]
baparams.append((n1,n2,r1,r2))
# generate dtype = LAMMPS type of each dihedral
# generate dparams = LAMMPS params for each dihedral type
@ -774,8 +804,8 @@ for atom1,atom2,atom3,atom4 in dlist:
if (c1,c2,c3,c4) in ddict: m,params = ddict[(c1,c2,c3,c4)]
elif (c4,c3,c2,c1) in ddict: m,params = ddict[(c4,c3,c2,c1)]
else:
print "Dihedral not found",atom1,atom2,atom3,atom4,c1,c2,c3,c4
sys.exit()
error("Dihedral not found: %d %d %d %d: %d %d %d %d" % \
(atom1,atom2,atom3,atom4,c1,c2,c3,c4))
if not flags[m]:
oneparams = params[4:]
@ -948,17 +978,12 @@ if nangles:
lines.append(line+'\n')
d.sections["Angle Coeffs"] = lines
#lines = []
#for i,one in enumerate(aparams):
# line = "%d %g %g %g" % (i+1,0.0,0.0,0.0)
# lines.append(line+'\n')
#d.sections["BondBond Coeffs"] = lines
#lines = []
#for i,one in enumerate(aparams):
# line = "%d %g %g %g %g" % (i+1,0.0,0.0,0.0,0.0)
# lines.append(line+'\n')
# d.sections["BondAngle Coeffs"] = lines
lines = []
for i,one in enumerate(baparams):
strone = [str(single) for single in one]
line = "%d %s" % (i+1,' '.join(strone))
lines.append(line+'\n')
d.sections["BondAngle Coeffs"] = lines
lines = []
for i,one in enumerate(alist):