def alignAtoms(al1,al2,sel1=None,sel2=None):
""" another interface to the align function
will align atoms in al2 to atoms in al1
optional: sel1: list of indices af atoms in al1 (does not have to be numpy.array)
optional: sel2: list of indices af atoms in al2 (does not have to be numpy.array)
lengths of these two selections have to be the same
"""
if sel1 == None:
sel1 = range(len(al1))
if sel2 == None:
sel2 = range(len(al2))
assert len(sel1) == len(sel2), 'Error: lenghts of the two selections in geometry.alignAtomsAngle is not the same: %d and %d' % (len(sel1), len(sel2))
# create a list of dumme atoms with the target orientations that we are aligning to
bl2 = []
for i in range(len(al2)):
b = atoms.Atom()
bl2.append(b)
for i in range(len(sel1)):
b = bl2[sel2[i]]
b.xyz = al1[sel1[i]].xyz.copy()
set1_orig = atoms.getXyzFromList(bl2)
set2_orig = atoms.getXyzFromList(al2)
set2, RMSD, RMSDnonsel, RMSDall = align( set1_orig, set2_orig, selection = numpy.array(sel2))
atoms.putXyzIntoList(al2,set2)
return RMSD
def alignBackboneAtoms(al1,al2):
"""aligns al2 to the backbone of al1
the two provided atoms list do not need to have the same number of atoms
but they have to have the same number of residues
returns al2 list"""
backbone = ['N','CA','C','O']
xyz2 = atoms.getXyzFromList(al2)
xyz1 = xyz2.copy()
rl1 = residues.makeList(al1)
rl2 = residues.makeList(al2)
selection = []
if len(rl1) != len(rl2):
sys.exit('Error in alignBackboneAtoms: the two list have different numebr of residues: %d and %d' % (len(rl1), len(rl2)))
for i in range(len(rl1)):
if rl1[i].rName == 'RES':
continue
r1 = rl1[i]
r2 = rl2[i]
for aName in backbone:
a1 = r1.atomWithName(aName)
a2 = r2.atomWithName(aName)
i2 = al2.index(a2)
selection.append(i2)
xyz1[i2] = a1.xyz
xyz3, RMSD, RMSDnonsel, RMSDall = align( xyz1, xyz2, selection = selection)
atoms.putXyzIntoList(al2,xyz3)
return al2
def getWaterBox(boxSize):
al = getSmallBox()
sA = defaults.waterBoxSize[0,:]
sB = defaults.waterBoxSize[1,:]
sC = defaults.waterBoxSize[2,:]
sO = defaults.waterBoxSize[3,:]
lA = boxSize[0,:]
lB = boxSize[1,:]
lC = boxSize[2,:]
lO = boxSize[3,:]
if lC[0]!=0 or lC[1]!=0 or lB[2]!=0 or lA[2]!=0:
print 'only can lay basic water box when certain coordinates are 0'
sys.exit(1)
if lA[1] != 0:
print 'only can lay basic water box when lA[1] is zero (simpler to implement)'
sys.exit(1)
if lB[0] < 0:
print 'only can lay basic water box when lB[0] < 0 is zero (simpler to implement)'
sys.exit(1)
if lA[0] < 0 or lB[1] < 0:
print 'only can lay basic water box when lA[0] > 0 and lB[1] > 0 (simpler to implement)'
sys.exit(1)
xyz = atoms.getXyzFromList(al)
xyz = xyz - sO + (sA+sB+sC)/2.0
atoms.putXyzIntoList(al,xyz)
nO = lO-(lA+lB+lC)/2.0
nABC = nO + lA+lB+lC
nal = []
for i in numpy.arange(nO[0],nABC[0],sA[0]):
for j in numpy.arange(nO[1],nABC[1],sB[1]):
for k in numpy.arange(nO[2],nABC[2],sC[2]):
vec = numpy.array([i,j,k])
nal.extend( periodic.copyTo(al, vec) )
# trim waters and renumber their residue numbers
print 'number of waters in the construction box: %d' % (len(nal)/3)
sel = []
rNo = 0
for a in nal:
if a.ffType.strip() == 'OW' and a.rName.strip() == 'WAT':
if periodic.isInsideBox(a.xyz, boxSize):
if len(a.bonds) != 2:
print 'this is not water!!!!! % s ' % str(a)
sys.exit(1)
h1 = a.bonds[0]
h2 = a.bonds[1]
rNo = rNo + 1
a.rNo = rNo
h1.rNo = rNo
h2.rNo = rNo
sel.extend([a,h1,h2])
atoms.renumberAtomsFrom(sel)
print 'number of waters in the produced box: %d' % (len(sel)/3)
return sel
def replicate(al,
boxSize,
na,
nb,
nc,
cutoff=2.0,
maxBonds=4,
includePeriodic=True):
'''na=nb=nc=1 would just keep the same atoms'''
putCoordinatesIntoBox(al, boxSize)
xyz = atoms.getXyzFromList(al).copy()
cal = copy.deepcopy(al)
# cell vectors are boxSize[i,:] for i 0,1,2
a = boxSize[0, :]
b = boxSize[1, :]
c = boxSize[2, :]
for i in range(1, na):
v = i * a
cal2 = copy.deepcopy(cal)
geometry.moveAtoms(cal2, v)
al.extend(cal2)
cal = copy.deepcopy(al)
for i in range(1, nb):
v = i * b
cal2 = copy.deepcopy(cal)
geometry.moveAtoms(cal2, v)
al.extend(cal2)
cal = copy.deepcopy(al)
for i in range(1, nc):
v = i * c
cal2 = copy.deepcopy(cal)
geometry.moveAtoms(cal2, v)
al.extend(cal2)
newbox = numpy.vstack([na * a, nb * b, nc * c, boxSize[3, :]])
putCoordinatesIntoBox(al, newbox)
bonds.findBonds(al, cutoff=cutoff, maxBonds=maxBonds)
if includePeriodic:
bonds.findBondsAcrossBoundary(al,
newbox,
cutoff=cutoff,
maxBonds=maxBonds)
return newbox
def findStericClash(al,distance = 3.0):
'''find pairs of atoms which are not connected by a bond or don't have a common neighbor which are closer than the given distance '''
from packages import kdtree
xyz = atoms.getXyzFromList(al)
kd = kdtree.KDTree(3,10) # dimension = 3, bucket size = 10
kd.set_coords(xyz)
counter = 0
for i in range(len(al)):
a = al[i]
kd.search(a.xyz, distance)
result_indices = kd.get_indices()
for j in result_indices:
if i<j:
if not a.lessThanThreeBondsFrom(al[j]):
print 'atoms %s (index %d) and %s (index %d) are at distance %f ' % (a, i, al[j],j,a.distance(al[j]))
counter += 1
print ' summary: in total found %d pairs of atoms (nonbonded or separated by more than two bonds) closer than %f' % (counter, distance)
def catbgf2xyz(catbgfFile,xyzFile,firstLabel = 1,keepFrames = []):
xyzlist = []
names = []
with open(catbgfFile) as f:
lines = []
counter = firstLabel
line = f.readline()
while line != '':
lines.append(line)
if line.startswith('END'):
al = bgf.readLines(lines)
if (keepFrames == []) or (counter in keepFrames):
xyz = atoms.getXyzFromList(al)
xyzlist.append(xyz)
names.append('%d'% counter)
print counter
counter += 1
lines = []
line = f.readline()
write(xyzFile,numpy.array(xyzlist),names=names,al=al)
def removeOverlappingWater(al,water):
"""remove waters which have oxygen closer than 2.5 to any atom in the list al"""
from packages import kdtree
radius = 2.5
kd = kdtree.KDTree(3,10) # dimension = 3, bucket size = 10
xyz = atoms.getXyzFromList(water)
oxygens = []
for i in range(len(water)):
a = water[i]
if a.ffType.strip() == 'OW' and a.rName.strip() == 'WAT':
oxygens.append(i)
kd.set_coords(xyz[oxygens,:])
watersToRemove = []
for a in al:
# test if there is any water near atom a
kd.search(a.xyz, radius)
# collect the results
result_indices = kd.get_indices()
watersToRemove.extend( list(result_indices))
watersToRemove = set(watersToRemove)
watersToRemove = list(watersToRemove)
keepwater = [True] * len(oxygens)
for i in watersToRemove:
keepwater[i] = False
rNo = 0
newwater = []
for i in range(len(oxygens)):
if keepwater[i]:
ox = water[oxygens[i]]
h1 = ox.bonds[0]
h2 = ox.bonds[1]
rNo = rNo + 1
ox.rNo = rNo
h1.rNo = rNo
h2.rNo = rNo
newwater.extend([ox,h1,h2])
return newwater
def generateLammpsData(al,
ff,
fileBase,
cell=None,
debug=False,
exceptResidues=[]):
"""denerates the data file with all the information for Lammps
only rectangular cells are supported
so cell is a list of
tree values [xrange, yrange,zrange] with center 0,0,0
or
4x3 numpy array with the cell size in the NAMD notation
"""
filescript = fileBase + '.in'
filedata = fileBase + '.data'
if debug:
print 'getting ready to write lammps input and datafiles: %s, %s' % (
filescript, filedata)
st = structure.Structure(al,
ff,
debug=debug,
exceptResidues=exceptResidues)
# find out which angles and types are actually used
# if the molecule is very flat bin style for neighbor crashes, so use nsq
useNsqNeighbor = False
xyz = atoms.getXyzFromList(al)
xyzmax = numpy.max(xyz, axis=0)
xyzmin = numpy.min(xyz, axis=0)
xyzRange = xyzmax - xyzmin
if min(xyzRange) < 2.5: useNsqNeighbor = True
# periodicity considerations
if cell == None:
isPeriodic = False
cellBoundary = 's s s'
xyzmin = xyzmin - ff.cutoffNonBond
xyzmax = xyzmax + ff.cutoffNonBond
cell = [
xyzmin[0], xyzmax[0], xyzmin[1], xyzmax[1], xyzmin[2], xyzmax[2]
]
else:
isPeriodic = True
cellBoundary = 'p p p'
if len(cell) == 3:
boxSize = numpy.zeros((4, 3))
boxSize[0, 0] = cell[0]
boxSize[1, 1] = cell[1]
boxSize[2, 2] = cell[2]
elif len(cell) == 4:
boxSize = cell
else:
sys.exit(
'Error: prepLammps in generateLammpsData: wrong input for cell dimensions (has to have length 3 or 4, but has %d'
% len(cell))
# need to make sure all the atoms are in the main cell
# make array with the box size in the NAMD notation
periodic.putCoordinatesIntoBox(al, boxSize)
# create list of 6 or 9 numbers xmin,xmax,xy... to specify lammps cell size
# lammps: "origin" at (xlo,ylo,zlo)
# 3 edge vectors starting from the origin given by
# A = (xhi-xlo,0,0);
# B = (xy,yhi-ylo,0);
# C = (xz,yz,zhi-zlo).
# check that the box has 0's in the right places:
if boxSize[0, 1] != 0 or boxSize[0, 2] != 0 or boxSize[
1, 2] != 0 or boxSize[0, 0] <= 0. or boxSize[
1, 1] <= 0.0 or boxSize[2, 2] <= 0.:
sys.exit(
'Error: prepLammps: cell vector A is not aligned with +x or B is not in xy plane: %s , but these are required by lammps'
% str(boxSize))
# lammps has pretty weird definition of the periodic cell, just look at hte lammps online page to understand this...
origin = boxSize[3, :] - (boxSize[0, :] + boxSize[1, :] +
boxSize[2, :]) / 2
xlo = origin[0]
ylo = origin[1]
zlo = origin[2]
lx = boxSize[0, 0]
ly = boxSize[1, 1]
lz = boxSize[2, 2]
xy = boxSize[1, 0]
xz = boxSize[2, 0]
yz = boxSize[2, 1]
xhi = xlo + lx
yhi = ylo + ly
zhi = zlo + lz
cell = [xlo, xhi, ylo, yhi, zlo, zhi]
if xy != 0 or xz != 0 or yz != 0:
cell.append(xy)
cell.append(xz)
cell.append(yz)
# variables describing pair styles:
#
# usedPairStyle -- vdw requested in the par file, morse or lj12-6
# isPeriodic
# doHydrogenBonds
# myHBondType - only defined if doHydrogenBonds is True
# pairStyleHybrid
# pairStyleVDW
# pairStyleCoul - only defined if usedPairStyle == 'morse'
# vdwtype
usedPairStyle = ff.atomTypes[st.sortedAtomLabels[0]].vdwType
# hbond type
if len(st.sortedHydrogenBondTypes) > 0 and ff.doHbonds:
doHydrogenBonds = True
if st.sortedHydrogenBondTypes[0].type == 'morse':
myHBondType = 'hbond/dreiding/morse'
elif st.sortedHydrogenBondTypes[0].type == 'lj12-10':
myHBondType = 'hbond/dreiding/lj'
else:
sys.exit('Erorr: unknown hydrogen bond type: %s' %
(st.sortedHydrogenBondTypes[0].type))
else:
doHydrogenBonds = False
# is this hybrid pair style?
if (not doHydrogenBonds) and usedPairStyle in ['lj12-6', 'exp6']:
pairStyleHybrid = False
else:
pairStyleHybrid = True
# prepare names
if usedPairStyle == 'lj12-6':
if isPeriodic:
pairStyleVDW = 'lj/charmm/coul/long/opt'
else:
pairStyleVDW = 'lj/charmm/coul/charmm'
elif usedPairStyle == 'exp6':
if isPeriodic:
pairStyleVDW = 'buck/coul/long'
else:
pairStyleVDW = 'buck/coul/cut'
elif usedPairStyle == 'morse':
pairStyleVDW = 'morse/opt'
if isPeriodic:
pairStyleCoul = 'coul/long'
else:
pairStyleCoul = 'coul/cut'
else:
sys.exit(
'Erorr: unknown VDW type in prepLammps.py (only lj12-6 and morse available now): %s'
% usedPairStyle)
# PREPROCESS EXPLICIT MIXING
# hybrid pair does not mix so we need to check if we are doing hydrogen bonds
pair_coeff_lines = []
if (
not pairStyleHybrid
) and usedPairStyle == 'lj12-6': # we only have to list offdiagonal VDW when it is requeted in the parameter file
for i, index in enumerate(st.sortedAtomLabels):
for j in range(i, len(st.sortedAtomLabels)):
jindex = st.sortedAtomLabels[j]
# first see, if we have to use off-diagonal rule, if not just compute it
if index + jindex in ff.offDiagVDWTypes:
params = ff.offDiagVDWTypes[index + jindex].lammps()
pair_coeff_lines.append(
'pair_coeff %d %d %s # %s-%s\n' %
(i + 1, j + 1, params, index, jindex))
elif jindex + index in ff.offDiagVDWTypes:
params = ff.offDiagVDWTypes[jindex + index].lammps()
pair_coeff_lines.append(
'pair_coeff %d %d %s # %s-%s\n' %
(i + 1, j + 1, params, index, jindex))
else: # for hybrid pair style we have to list the offdiagonal VDW always
if usedPairStyle == 'morse': # for morse coulomb is not included in the pair style but via hybrid
pair_coeff_lines.append('pair_coeff * * %s\n' % pairStyleCoul)
for i, index in enumerate(st.sortedAtomLabels):
for j in range(i, len(st.sortedAtomLabels)):
jindex = st.sortedAtomLabels[j]
# first see, if we have to use off-diagonal rule, if not just compute it
if index + jindex in ff.offDiagVDWTypes:
params = ff.offDiagVDWTypes[index + jindex].lammps()
elif jindex + index in ff.offDiagVDWTypes:
params = ff.offDiagVDWTypes[jindex + index].lammps()
else: # computing the diagonal rule here
bi = ff.atomTypes[index] # these are atom
bj = ff.atomTypes[jindex]
params = bi.mixWith(bj, ff.mean).lammps()
if pairStyleHybrid:
pair_coeff_lines.append(
'pair_coeff %d %d %s %s # %s-%s\n' %
(i + 1, j + 1, pairStyleVDW, params, index, jindex))
else:
pair_coeff_lines.append(
'pair_coeff %d %d %s # %s-%s\n' %
(i + 1, j + 1, params, index, jindex))
if doHydrogenBonds:
myHBondPower = st.sortedHydrogenBondTypes[0].power
for b in st.sortedHydrogenBondTypes:
bd = st.usedAtomLabels[b.donor] + 1
bh = st.usedAtomLabels[b.hydrogen] + 1
ba = st.usedAtomLabels[b.acceptor] + 1
if bd <= ba:
flag = 'i'
bi = bd
bj = ba
else:
flag = 'j'
bi = ba
bj = bd
pair_coeff_lines.append(
'pair_coeff %d %d %s %d %s %s # donor:%s hydrogen:%s acceptor:%s \n'
% (bi, bj, myHBondType, bh, flag, b.lammps(), b.donor,
b.hydrogen, b.acceptor))
# OUTPUTTING
# output the stuff
if debug: print 'writing lammps input and datafile'
# the script file
with open(filescript, 'w') as script:
script.write('boundary %s \n' % cellBoundary)
script.write('units real \n')
if useNsqNeighbor: script.write('neighbor 2.0 nsq\n')
if ff.cutoffNonBond > 15.0:
# the default number of neighbors in lammps is 2000
# the number of atoms in radius r is ~0.4*r^3, let's use 50% more
estimate = int(0.6 * math.pow(ff.cutoffNonBond, 3.0))
bound = len(al) + 10
neighborone = max(2000, min(estimate, bound))
neighborpage = 20 * neighborone
script.write('neigh_modify one %d page %d\n' %
(neighborone, neighborpage))
pass
#script.write('neigh_modify delay 10 every 1 check yes one 4000 page 40000\n')
script.write(' \n')
script.write('atom_style full \n')
# BOND STYLE
if len(st.usedBondTypes) > 0:
script.write('bond_style harmonic\n')
else:
script.write('bond_style none \n')
# ANGLE STYLE
if len(st.usedAngleTypes) > 0:
if st.sortedAngleTypes[0].type == 'harmonic':
script.write('angle_style harmonic \n')
else: # cosine angles as in dreiding
script.write(
'angle_style hybrid cosine/periodic cosine/squared \n')
else:
script.write('angle_style none \n')
# TORSION STYLE
if len(st.usedTorsionTypes) > 0:
script.write('dihedral_style harmonic \n')
else:
script.write('dihedral_style none \n')
# INVERSION STYLE
if len(st.usedInversionTypes) > 0:
if st.sortedInversionTypes[0].type == 'amber':
script.write('improper_style cvff \n')
else: # dreiding inversion
script.write('improper_style umbrella \n')
else:
script.write('improper_style none \n')
script.write(' \n')
# PAIR STYLE
if not pairStyleHybrid:
if usedPairStyle == 'lj12-6':
script.write(
'pair_style %s %f %f \n' %
(pairStyleVDW, ff.splineNonBond, ff.cutoffNonBond))
script.write(
'pair_modify mix %s \n' %
ff.mean) # note that hte hybrid style does not do mixing
elif usedPairStyle == 'exp6':
script.write('pair_style %s %f \n' %
(pairStyleVDW, ff.cutoffNonBond))
else:
sys.exit(
'Error in prepLammps. One should never get to this part of code, but usedPairStyle is :%s'
% usedPairStyle)
else:
pairStyleLine = 'pair_style hybrid/overlay'
if usedPairStyle == 'lj12-6':
pairStyleLine += ' %s %f %f' % (pairStyleVDW, ff.splineNonBond,
ff.cutoffNonBond)
elif usedPairStyle == 'morse':
pairStyleLine += ' %s %f' % (pairStyleVDW, ff.cutoffNonBond)
pairStyleLine += ' %s %f' % (pairStyleCoul, ff.cutoffNonBond)
else:
sys.exit(
'Erorr: unknown VDW type in prepLammps.py (only lj12-6 and morse available now): %s'
% usedPairStyle)
if doHydrogenBonds:
pairStyleLine += ' %s %d %f %f %f \n' % (
myHBondType, myHBondPower, ff.splineHBond, ff.cutoffHBond,
ff.angleHBond)
pairStyleLine += ' \n'
script.write(pairStyleLine)
if isPeriodic:
script.write('kspace_style pppm 1e-4 \n')
script.write('dielectric %f \n' % ff.dielectric)
if ff.special14lj == 1.0 and ff.special14coul == 1.0:
script.write('special_bonds dreiding \n')
elif ff.special14lj == 0.5 and ff.special14coul == 1.0 / 1.2:
script.write('special_bonds amber \n')
else:
print >> sys.stderr, 'special14lj %f and special14coul %f is neither dreiding nor amber ' % (
ff.special14lj, ff.special14coul)
sys.exit(1)
script.write(' \n')
script.write('read_data %s \n' % filedata)
script.write(' \n')
script.write(
'#### alternatively read coordinates from the latest (*) restart file \n'
)
script.write('# read_restart restart.*\n')
script.write(' \n')
for line in pair_coeff_lines:
script.write(line)
# write the run information into the script file
# define computes
script.write(' \n')
script.write('variable step equal step \n')
script.write('variable ebond equal ebond \n')
script.write('variable eangle equal eangle \n')
script.write('variable edihed equal edihed \n')
script.write('variable eimp equal eimp \n')
script.write('variable emol equal emol \n')
script.write('variable ecoul equal ecoul \n')
# the values reported by hbond computes are not correct, so have to use some global variables
# try 1 after update
#if doHydrogenBonds:
# script.write('compute hbond all pair hbond/dreiding/%s \n' % myHBondType)
# script.write('variable hbond equal c_hbond[2] \n')
# script.write('variable counthbond equal c_hbond[1] \n')
#else:
# script.write('variable hbond equal 0.0 \n')
# script.write('variable counthbond equal 0.0 \n')
#script.write('variable evdwl equal evdwl-v_hbond \n') # NOTE: thermo evdwl already contains hbond
# try 2
script.write('compute evdwl all pair %s evdwl \n' %
pairStyleVDW)
script.write('variable evdwl equal c_evdwl \n'
) # NOTE: thermo evdwl already contains hbond
if doHydrogenBonds:
script.write('compute hbondevdwl all pair %s evdwl \n' %
myHBondType)
script.write('variable hbond equal c_hbondevdwl \n')
script.write('compute hbond all pair %s \n' % myHBondType)
script.write('variable counthbond equal c_hbond[1] \n')
else:
script.write('variable hbond equal 0.0 \n')
script.write('variable counthbond equal 0.0 \n')
script.write('variable elong equal elong \n')
script.write('variable epair equal epair \n')
script.write('variable pe equal pe \n')
script.write('variable ke equal ke \n')
script.write('variable etotal equal etotal \n')
script.write('variable temp equal temp \n')
script.write('variable press equal press \n')
script.write('variable fmax equal fmax \n')
script.write(' \n')
script.write('thermo 100 \n')
script.write(
'thermo_style custom step ebond eangle edihed eimp emol ecoul v_evdwl v_hbond v_counthbond elong epair pe ke etotal temp press fmax\n'
)
script.write(' \n')
# fixed atoms
# there is 2048 characters per line limit in lammps
fixed = [a for a in al if a.fixed]
if len(fixed) > 0:
groupLines = makeGroupLines(fixed, 'freezeatoms')
script.write(groupLines)
script.write(
'fix freeze freezeatoms setforce 0.0 0.0 0.0')
script.write('\n')
# sample commands
script.write('\n')
script.write('#### output the (wrapped) coordinates \n')
script.write(
'# dump 1 all custom 100 dump.lammpstrj id type x y z vx vy vz \n'
)
script.write('# dump_modify 1 sort id \n')
script.write('\n')
script.write('#### minimization \n')
script.write('# minimize 0.0 0.0 100 10000 \n')
script.write('\n')
script.write('#### initialization of velocities \n')
script.write(
'# velocity all create 300.0 4928459 mom yes rot yes dist gaussian\n'
)
script.write('\n')
script.write('#### nve run \n')
script.write('# timestep 1 \n')
script.write('# fix 1 all nve \n')
script.write('# run 1000 \n')
script.write(' \n')
script.write('#### write restart file (* gets replaced by timestep)\n')
script.write('# write_restart restart.*\n')
script.write(' \n')
# writing the data file
with open(filedata, 'w') as out:
# header of the data file
out.write('Generated by prepLammps.py, %s@%s on %s\n\n' %
(os.getenv('LOGNAME'), os.getenv('HOSTNAME'),
time.strftime('%X %x %Z')))
out.write('%d atoms\n' % len(al))
out.write('%d bonds\n' % len(st.bonds))
out.write('%d angles\n' % len(st.angles))
out.write('%d dihedrals\n' % len(st.torsions))
out.write('%d impropers\n\n' % len(st.inversions))
out.write('%d atom types\n' % len(st.sortedAtomLabels))
out.write('%d bond types\n' % len(st.sortedBondTypes))
out.write('%d angle types\n' % len(st.sortedAngleTypes))
out.write('%d dihedral types\n' % len(st.sortedTorsionTypes))
out.write('%d improper types\n\n' % len(st.sortedInversionTypes))
out.write('%f %f xlo xhi\n' % (cell[0], cell[1]))
out.write('%f %f ylo yhi\n' % (cell[2], cell[3]))
out.write('%f %f zlo zhi\n' % (cell[4], cell[5]))
if len(cell) == 9:
out.write('%f %f %f xy xz yz\n' % (cell[6], cell[7], cell[8]))
# atom types
out.write('\nMasses\n\n')
for i, b in enumerate(st.sortedAtomLabels):
bt = ff.atomTypes[b]
out.write('%d %f # %s\n' % (i + 1, bt.mass, b))
# vdw parameters and hydrogen bonds parameters
# bond Types
if not pairStyleHybrid:
out.write('\nPair Coeffs\n\n')
for i, b in enumerate(st.sortedAtomLabels):
bt = ff.atomTypes[b]
out.write('%d %s # %s\n' % (i + 1, bt.lammps(), b))
# bond Types
if len(st.sortedBondTypes) > 0:
out.write('\nBond Coeffs\n\n')
for i, bi in enumerate(st.sortedBondTypes):
out.write('%d %s\n' % (i + 1, bi.lammps()))
# angle Types
if len(st.sortedAngleTypes) > 0:
out.write('\nAngle Coeffs\n\n')
for i, bi in enumerate(st.sortedAngleTypes):
out.write('%d %s\n' % (i + 1, bi.lammps()))
# torsion Types
if len(st.sortedTorsionTypes) > 0:
out.write('\nDihedral Coeffs\n\n')
for i, bi in enumerate(st.sortedTorsionTypes):
out.write('%d %s\n' % (i + 1, bi.lammps()))
# inversion Types
if len(st.sortedInversionTypes) > 0:
out.write('\nImproper Coeffs\n\n')
for i, bi in enumerate(st.sortedInversionTypes):
out.write('%d %s\n' % (i + 1, bi.lammps()))
# atoms
out.write('\nAtoms\n\n')
for a in al:
atomtypeindex = st.usedAtomLabels[a.ffType] + 1
out.write('%d 0 %d %.10f %.10f %.10f %.10f # %s\n' %
(a.aNo, atomtypeindex, a.charge, a.xyz[0], a.xyz[1],
a.xyz[2], a))
# bonds
out.write('\nBonds\n\n')
for i, bi in enumerate(st.bonds):
out.write(
'%d %d %d %d\n' %
(i + 1, st.usedBondTypes[bi.type] + 1, bi.i.aNo, bi.j.aNo))
# angles
out.write('\nAngles\n\n')
for i, bi in enumerate(st.angles):
out.write('%d %d %d %d %d\n' % (i + 1, st.usedAngleTypes[bi.type] +
1, bi.i.aNo, bi.j.aNo, bi.k.aNo))
# torsion
out.write('\nDihedrals\n\n')
for i, bi in enumerate(st.torsions):
out.write('%d %d %d %d %d %d\n' %
(i + 1, st.usedTorsionTypes[bi.type] + 1, bi.i.aNo,
bi.j.aNo, bi.k.aNo, bi.l.aNo))
# inversions
out.write('\nImpropers\n\n')
for i, bi in enumerate(st.inversions):
if bi.type.type == 'amber':
out.write('%d %d %d %d %d %d\n' %
(i + 1, st.usedInversionTypes[bi.type] + 1, bi.j.aNo,
bi.k.aNo, bi.i.aNo, bi.l.aNo))
elif bi.type.type == 'dreiding':
out.write('%d %d %d %d %d %d\n' %
(i + 1, st.usedInversionTypes[bi.type] + 1, bi.i.aNo,
bi.j.aNo, bi.k.aNo, bi.l.aNo))
else:
print >> sys.stderr, 'Unknown improper type for lammps (probably unimplemented yet) %s ' % bi.type.type
sys.exit(1)
if debug:
print 'done writing lammps input and datafiles: %s, %s' % (filescript,
filedata)
return st
def copyTo(al, vec):
nal = copy.deepcopy(al)
xyz = atoms.getXyzFromList(nal)
xyz = xyz + vec
atoms.putXyzIntoList(nal, xyz)
return nal
def setAtoms(self, al, append=True):
xyz = atoms.getXyzFromList(al)
self.set(xyz, append=append)
def moveAtoms(al, vector):
xyz = atoms.getXyzFromList(al)
xyz = xyz + vector
atoms.putXyzIntoList(al, xyz)
def rotateAtoms(al, axis,angle,origin = None, radians=False):
xyz = atoms.getXyzFromList(al)
xyz = rotate(xyz,axis,angle,origin = origin, radians=radians)
atoms.putXyzIntoList(al, xyz)
def writeAtomList(filename,al):
xyz = atoms.getXyzFromList(al)
write(filename,numpy.array([xyz]),names=[filename],al=al)