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Bends of 180 are now linear in cosine, cleaner code
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@lvduyfhu
lvduyfhu committed Jan 19, 2017
1 parent 89a4e73 commit 5ba42ed
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Showing 2 changed files with 110 additions and 18 deletions.
6 changes: 6 additions & 0 deletions quickff/program.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,6 +189,12 @@ def average_pars(self):
self.valence.set_params(master.index, fc=fc, rv0=rv, m=m)
for islave in master.slaves:
self.valence.set_params(islave, fc=fc, rv0=rv, m=m)
elif master.kind==5:#chebychev
assert pars.shape[1]==1
fc = pars[:,0].mean()
self.valence.set_params(master.index, fc=fc)
for islave in master.slaves:
self.valence.set_params(islave, fc=fc)
else:
raise NotImplementedError

Expand Down
122 changes: 104 additions & 18 deletions quickff/valence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,14 @@
#
#--
from molmod.units import *
from molmod.ic import bend_angle, _bend_angle_low, dihed_angle, _dihed_angle_low

from yaff.pes.ff import ForceField, ForcePartValence
from yaff.pes.parameters import *
from yaff.pes.vlist import ValenceList
from yaff.pes.vlist import Harmonic, PolyFour, Fues, Cosine, Cross
from yaff.pes.vlist import Harmonic, PolyFour, Fues, Cosine, Cross, Chebychev1
from yaff.pes.iclist import InternalCoordinateList
from yaff.pes.iclist import Bond, BendAngle, DihedCos, DihedAngle, OopDist, SqOopDist
from yaff.pes.iclist import Bond, BendAngle, BendCos, DihedCos, DihedAngle, OopDist, SqOopDist
from yaff.pes.dlist import DeltaList
from yaff.sampling.harmonic import estimate_cart_hessian

Expand Down Expand Up @@ -140,6 +141,15 @@ def to_string(self, valence, max_name=38, max_line=72):
]
units = [self.units[1], self.units[2], 'au']
ndigits = [(4,3), (4,3), (1,0)]
elif self.kind==5:#chebychev
fcs = pars[:,0]
means = [fcs.mean()]
stds = [fcs.std()]
formats = [
'fc = %%4s %s %%3s' %(u"\u00B1"),
]
units = [self.units[0]]
ndigits = [(4,3)]
#convert term pars to string
line = '%s (%s)' %(
self.basename[:max_line],
Expand Down Expand Up @@ -213,9 +223,10 @@ def add_term(self, pot, ics, atypes, tasks, units):
#define the name
if len(ics)==1:
tmp = {
(0,0) : 'BondHarm/', (2,0) : 'BendAHarm/' ,
(4,4) : 'Torsion/' , (3,1) : 'TorsC2Harm/',
(10,0): 'Oopdist/' , (11,0): 'SqOopdist/' ,
(0,0) : 'BondHarm/' ,
(1,5) : 'BendCLin/', (2,0) : 'BendAHarm/' ,
(4,4) : 'Torsion/' , (3,1) : 'TorsC2Harm/',
(10,0): 'Oopdist/' , (11,0): 'SqOopdist/' ,
}
prefix = tmp[(ics[0].kind, pot.kind)]
suffix = ''
Expand Down Expand Up @@ -257,7 +268,11 @@ def add_term(self, pot, ics, atypes, tasks, units):
args = [(None,)*len(units)] + ics
else:
args = [None,]*len(units) + ics
ForcePartValence.add_term(self, pot(*args))
if pot.kind==5:
#in case of chebychev, set sign to +1
ForcePartValence.add_term(self, pot(*args,sign=1.0))
else:
ForcePartValence.add_term(self, pot(*args))
return term

def modify_term(self, term_index, pot, ics, basename, tasks, units):
Expand Down Expand Up @@ -331,18 +346,46 @@ def init_bend_terms(self):
'''
Initialize all bend terms in the system based on the bends attribute
of the system instance. All bend terms are given harmonic
potentials.
potentials either in the angle or the cosine of the angle.
'''
with log.section('VAL', 3, 'Initializing'):
ffatypes = [self.system.ffatypes[fid] for fid in self.system.ffatype_ids]
#get the angle terms
nbends = 0
ffatypes = [self.system.ffatypes[fid] for fid in self.system.ffatype_ids]
angles = {}
for angle in self.system.iter_angles():
angle, types = term_sort_atypes(ffatypes, angle, 'angle')
units = ['kjmol/rad**2', 'deg']
self.add_term(Harmonic, [BendAngle(*angle)], types, ['PT_ALL', 'HC_FC_DIAG'], units)
nbends += 1
log.dump('Added %i Harmonic bend terms' %nbends)
angle, types = term_sort_atypes(ffatypes, angle, 'dihedral')
if types in angles.keys():
angles[types].append(angle)
else:
angles[types] = [angle]
#loop over all distinct angle types
nabends = 0
ncbends = 0
for types, bends in angles.iteritems():
do_cos = False
for i, bend in enumerate(bends):
if self.system.cell.nvec>0:
d10 = self.system.pos[bend[0]] - self.system.pos[bend[1]]
d12 = self.system.pos[bend[2]] - self.system.pos[bend[1]]
self.system.cell.mic(d10)
self.system.cell.mic(d12)
if _bend_angle_low(d10, d12, 0)[0] > 175*deg:
do_cos = True
break
else:
rs = np.array([self.system.pos[j] for j in bend])
if bend_angle(rs)[0]>175*deg:
do_cos = True
break
#add term harmonic in angle or cos(angle)
for bend in bends:
if do_cos:
term = self.add_term(Chebychev1, [BendCos(*bend)], types, ['HC_FC_DIAG'], ['kjmol'])
ncbends += 1
else:
self.add_term(Harmonic, [BendAngle(*bend)], types, ['PT_ALL', 'HC_FC_DIAG'], ['kjmol/rad**2', 'deg'])
nabends += 1
log.dump('Added %i bend terms harmonic in the angle and %i bend terms linear in cos(angle)' %(nabends, ncbends))

def init_dihedral_terms(self, thresshold=20*deg):
'''
Expand All @@ -360,7 +403,6 @@ def init_dihedral_terms(self, thresshold=20*deg):
'''
with log.section('VAL', 3, 'Initializing'):
#get all dihedrals
from molmod.ic import dihed_angle, _dihed_angle_low
ffatypes = [self.system.ffatypes[fid] for fid in self.system.ffatype_ids]
dihedrals = {}
for dihedral in self.system.iter_dihedrals():
Expand All @@ -374,6 +416,7 @@ def init_dihedral_terms(self, thresshold=20*deg):
for types, diheds in dihedrals.iteritems():
psi0s = np.zeros(len(diheds), float)
ms = np.zeros(len(diheds), float)
bendskip = False
for i, dihed in enumerate(diheds):
if self.system.cell.nvec>0:
d10 = self.system.pos[dihed[0]] - self.system.pos[dihed[1]]
Expand All @@ -382,13 +425,27 @@ def init_dihedral_terms(self, thresshold=20*deg):
self.system.cell.mic(d10)
self.system.cell.mic(d12)
self.system.cell.mic(d23)
#check if bending angle is not 180 deg
bend012 = _bend_angle_low(d10, d12, 0)[0]
bend123 = _bend_angle_low(d12, d23, 0)[0]
if bend012>175*deg or bend123>175*deg:
bendskip = True
continue
psi0s[i] = _dihed_angle_low(d10, d12, d23, 0)[0]
else:
rs = np.array([self.system.pos[j] for j in dihed])
bend012 = bend_angle(rs[:3])[0]
bend123 = bend_angle(rs[1:4])[0]
if bend012>175*deg or bend123>175*deg:
bendskip = True
continue
psi0s[i] = dihed_angle(rs)[0]
n1 = len(self.system.neighs1[dihed[1]])
n2 = len(self.system.neighs1[dihed[2]])
ms[i] = get_multiplicity(n1, n2)
if bendskip:
log.warning('Dihedral for %s contains bend angle close to 180 deg, skipping' %('.'.join(types)))
continue
if np.isnan(ms).any() or ms.std()>1e-3:
ms_string = str(ms)
if np.isnan(ms).any():
Expand Down Expand Up @@ -545,7 +602,14 @@ def get_hessian_contrib(self, index, fc=None):
val = ForcePartValence(self.system)
kind = self.vlist.vtab[index]['kind']
masterslaves = [index]+self.terms[index].slaves
if kind==4:#Cosine
if kind==5:#Chebychev
k = self.get_params(index, only='fc')
if fc is not None: k = fc
for jterm in masterslaves:
ics = self.terms[jterm].ics
args = (k,) + tuple(ics)
val.add_term(Chebychev1(*args,sign=1.0))
elif kind==4:#Cosine
m, k, rv = self.get_params(index)
if fc is not None: k = fc
for jterm in masterslaves:
Expand Down Expand Up @@ -603,6 +667,8 @@ def set_params(self, term_index, fc=None, rv0=None, rv1=None, m=None,
if m is not None: term['par0'] = m
if fc is not None: term['par1'] = fc
if rv0 is not None: term['par2'] = rv0
elif term['kind'] in [5]:#['Chebychev1']
if fc is not None: term['par0'] = fc
elif term['kind'] in [3]:#['Cross']
if fc is not None: term['par0'] = fc
if rv0 is not None: term['par1'] = rv0
Expand Down Expand Up @@ -633,6 +699,10 @@ def get_params(self, term_index, only='all'):
elif only.lower()=='fc': return term['par1']
elif only.lower()=='rv': return term['par2']
else: raise ValueError('Invalid par kind definition %s' %only)
elif term['kind'] in [5]:#['Chebychev']
if only.lower()=='all': return term['par0'],
elif only.lower()=='fc': return term['par0']
else: raise ValueError('Invalid par kind definition %s' %only)
elif term['kind'] in [3]:#['Cross']
if only.lower()=='all': return term['par0'], term['par1'], term['par2']
elif only.lower()=='fc': return term['par0']
Expand Down Expand Up @@ -660,6 +730,8 @@ def is_negligible(self, term_index):
return abs(term['par1']) < 1e-6*kjmol
elif term['kind'] in [3]: # ['Cross']
return abs(term['par0']) < 1e-6*kjmol
elif term['kind']==5 and self.terms[term_index].ics[0].kind==1: #linear in cos(angle):
return abs(term['par0']) < 1e-6*kjmol
else:
raise NotImplementedError(
'is_negligible not implemented for Yaff %s term' % term['kind'])
Expand Down Expand Up @@ -693,7 +765,7 @@ def dump_logger(self, print_level=1):
with log.section('', print_level):
sequence = [
'bondharm',
'bendaharm', 'bendcharm', 'bendcos',
'bendaharm', 'bendclin', 'bendcharm', 'bendcos',
'torsion', 'torsc2harm', 'dihedharm',
'oopdist', 'cross'
]
Expand Down Expand Up @@ -734,6 +806,20 @@ def _bendaharm_to_yaff(self):
))
return ParameterSection(prefix, definitions={'UNIT': units, 'PARS': pars})

def _bendclin_to_yaff(self):
'construct a BENDCLIN section of a yaff parameter file'
prefix = 'BENDCLIN'
units = ParameterDefinition('UNIT', lines=['A kjmol'])
pars = ParameterDefinition('PARS')
for i, master in enumerate(self.iter_masters(label=prefix)):
if self.is_negligible(i): continue
ffatypes = master.basename.split('/')[1].split('.')
K, = self.get_params(master.index)
pars.lines.append('%8s %8s %8s %.10e' %(
ffatypes[0], ffatypes[1], ffatypes[2], K/kjmol
))
return ParameterSection(prefix, definitions={'UNIT': units, 'PARS': pars})

def _bendcharm_to_yaff(self):
'construct a BENDCHARM section of a yaff parameter file'
prefix = 'BENDCHARM'
Expand Down Expand Up @@ -887,7 +973,7 @@ def dump_yaff(self, fn):
sections = [
self._bonds_to_yaff(),
self._bendaharm_to_yaff(), self._bendcharm_to_yaff(),
self._bendcos_to_yaff(),
self._bendcos_to_yaff(), self._bendclin_to_yaff(),
self._torsions_to_yaff(), self._torsc2harm_to_yaff(),
self._dihedharm_to_yaff(),
self._opdists_to_yaff(),self._sqopdists_to_yaff(),
Expand Down

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