elements = {}; atom_types = []; bond_types = []; angle_types = []; dihedral_types = []

for line in open(parameter_file):

columns = line.split()

if not columns: continue

if columns[0]=='atom':

m = re.match('atom +(\d+) +(\d+) +(\S+) +"([^"]+)" +(\d+) +(\S+) +(\d+)', line)

atom_type = utils.Struct(index=int(m.group(1)), index2=int(m.group(2)), element_name=m.group(3), notes=m.group(4), element=int(m.group(5)), mass=float(m.group(6)), bond_count=int(m.group(7) ) )

if atom_type.element not in elements: elements[atom_type.element] = []

elements[atom_type.element].append(atom_type)

if '(UA)' in atom_type.notes:

atom_type.element = 0 #reject united-atom parameters

atom_types.append(atom_type)

elif columns[0]=='vdw':

atom_types[int(columns[1])-1].vdw_r = max( float(columns[2]), 1.0)

atom_types[int(columns[1])-1].vdw_e = max( float(columns[3]), 0.01)

elif columns[0]=='charge':

atom_types[int(columns[1])-1].charge = float(columns[2])

elif columns[0]=='bond':

bond_types.append( utils.Struct(index2s=tuple([int(s) for s in columns[1:3]]),e=float(columns[3]),r=float(columns[4])) )

elif columns[0]=='angle':

angle_types.append( utils.Struct(index2s=tuple([int(s) for s in columns[1:4]]),e=float(columns[4]),angle=float(columns[5])) )

elif columns[0]=='torsion':

dihedral_types.append( utils.Struct(index2s=tuple([int(s) for s in columns[1:5]]),e=tuple([float(s) for s in columns[5::3]])) )

if len(dihedral_types[-1].e)==3:

dihedral_types[-1].e = dihedral_types[-1].e + (0.,)

elements, atom_types, bond_types, angle_types, dihedral_types = parse_opls_parameters(opls_parameter_file)

atom_types_by_element_and_bond_count = {}

for a in atom_types:

if (a.element, a.bond_count) not in atom_types_by_element_and_bond_count:

atom_types_by_element_and_bond_count[(a.element, a.bond_count)] = []

atom_types_by_element_and_bond_count[(a.element, a.bond_count)].append(a)

atomic_number = {'H':1, 'C':6, 'N':7}

for a in atoms:

a.type = atom_types_by_element_and_bond_count[(atomic_number[a.element],len(a.bonded))][0]

dihedral_types_by_index2 = dict([ (t.index2s,t) for t in dihedral_types] + [ (t.index2s[::-1],t) for t in dihedral_types])

angle_types_by_index2 = dict([ (t.index2s,t) for t in angle_types] + [ (t.index2s[::-1],t) for t in angle_types])

bond_types_by_index2 = dict([ (t.index2s,t) for t in bond_types] + [ (t.index2s[::-1],t) for t in bond_types])

def get_bond_type(options):

for o1 in options[0]:

for o2 in options[1]:

if (o1.index2, o2.index2) in bond_types_by_index2:

return o1, o2

for b in bonds:

options = [atom_types_by_element_and_bond_count[(atomic_number[a.element],len(a.bonded))] for a in b.atoms]

if not get_bond_type(options):

print 'No bond type for', b

for ii in range(1000):

b = random.choice(bonds)

if (b.atoms[0].type.index2, b.atoms[1].type.index2) not in bond_types_by_index2:

options = [atom_types_by_element_and_bond_count[(atomic_number[a.element],len(a.bonded))] for a in b.atoms]

if get_bond_type(options):

b.atoms[0].type, b.atoms[1].type = get_bond_type(options)

def missing_params(close_ok):

missing_count = 0

atom_badness = [0 for a in atoms]

for b in bonds:

if (b.atoms[0].type.index2, b.atoms[1].type.index2) not in bond_types_by_index2:

missing_count += 100

for atom in b.atoms:

atom_badness[atom.index-1] += 1

for a in angles:

if tuple([atom.type.index2 for atom in a.atoms]) not in angle_types_by_index2:

missing_count += 2

for atom in a.atoms:

atom_badness[atom.index-1] += 1

for d in dihedrals:

if tuple([a.type.index2 for a in d.atoms]) not in dihedral_types_by_index2 and not (close_ok and (0,d.atoms[1].type.index2,d.atoms[2].type.index2,0) in dihedral_types_by_index2):

missing_count += 1

for atom in d.atoms:

atom_badness[atom.index-1] += 1

return missing_count, atoms[atom_badness.index(max(atom_badness))]

def anneal_params(T_max, steps, close_ok):

best_error, worst_atom = missing_params(close_ok)

for T in numpy.arange(T_max,0.,-T_max/steps):

a = worst_atom if random.random()<0.8 else random.choice(atoms)

old_type = a.type

a.type = random.choice(atom_types_by_element_and_bond_count[(atomic_number[a.element],len(a.bonded))])

error, worst_atom = missing_params(close_ok)

#print (best_error-error)

if error < best_error or random.random() < math.exp( (best_error-error)/T ):

best_error = error

else:

a.type = old_type

best_types = None

best_error = missing_params(False)[0]

for i in range(5):

anneal_params(1.,1000,False)

anneal_params(0.1,1000,True)

error = missing_params(False)[0]

if error < best_error:

best_types = [a.type for a in atoms]

error = best_error

for i,a in enumerate(atoms):

if best_types: a.type = best_types[i]

print a.type.notes

print missing_params(True)

c1,c2,c3 = 0,0,0

for b in bonds:

if (b.atoms[0].type.index2, b.atoms[1].type.index2) not in bond_types_by_index2:

c1 += 1

for a in angles:

if tuple([atom.type.index2 for atom in a.atoms]) not in angle_types_by_index2:

c2 += 1

for d in dihedrals:

if tuple([a.type.index2 for a in d.atoms]) not in dihedral_types_by_index2:

c3 += 1

if (0,d.atoms[1].type.index2,d.atoms[2].type.index2,0) in dihedral_types_by_index2:

c3 -= 1

print c1, c2, c3

try:

bond_types_used = [ bond_types_by_index2[(b.atoms[0].type.index2,b.atoms[1].type.index2)] for b in bonds]

except: return None

for i,b in enumerate(bonds): b.e = bond_types_used[i].e

angle_types_used = []

for a in angles:

index2s = tuple([atom.type.index2 for atom in a.atoms])

if index2s in angle_types_by_index2:

angle_types_used.append(angle_types_by_index2[index2s])

else:

angle_types_used.append( utils.Struct(angle=180., e=0.) )

for i,a in enumerate(angles): a.e = angle_types_used[i].e

dihedral_types_used = []

for d in dihedrals:

index2s = tuple([a.type.index2 for a in d.atoms])

if index2s in dihedral_types_by_index2:

dihedral_types_used.append(dihedral_types_by_index2[index2s])

else:

dihedral_types_used.append( utils.Struct(e=(0.,0.,0.,0.)) )

for i,d in enumerate(dihedrals): d.e = dihedral_types_used[i].e

for a in atoms:

a.charge = a.type.charge

net_charge = sum([a.charge for a in atoms])

overcharged_count = len( [a for a in atoms if a.charge*net_charge>0] )

for a in atoms:

if a.charge*net_charge>0:

a.charge -= net_charge/overcharged_count

bond_types, angle_types, dihedral_types = starting_params

atom_types = [a.type for a in atoms]

atom_types_used = dict( [(t,True) for t in atom_types] )

bond_types_used = dict( [(t,True) for t in bond_types] )

angle_types_used = dict( [(t,True) for t in angle_types] )

dihedral_types_used = dict( [(t,True) for t in dihedral_types] )

atom_type_numbers = dict( [(t,i+1) for i,t in enumerate(atom_types_used)] )

bond_type_numbers = dict( [(t,i+1) for i,t in enumerate(bond_types_used)] )

angle_type_numbers = dict( [(t,i+1) for i,t in enumerate(angle_types_used)] )

dihedral_type_numbers = dict( [(t,i+1) for i,t in enumerate(dihedral_types_used)] )

box_size = (100,100,100)

os.chdir('lammps')

f = open(run_name+'.data', 'w')

f.write('''LAMMPS Description

'''+str(len(atoms))+''' atoms

'''+str(len(bonds))+''' bonds

'''+str(len(angles))+''' angles

'''+str(len(dihedrals))+''' dihedrals

0 impropers

'''+str(len(atom_types_used))+''' atom types

'''+str(len(bond_types_used))+''' bond types

'''+str(len(angle_types_used))+''' angle types

'''+str(len(dihedral_types_used))+''' dihedral types

0 improper types

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom_type_numbers[t], t.mass) for t in atom_types_used]))+'''

Pair Coeffs

'''+('\n'.join(["%d\t%f\t%f" % (atom_type_numbers[t], t.vdw_e, t.vdw_r) for t in atom_types_used])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (bond_type_numbers[t], t.e, t.r) for t in bond_types_used]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (angle_type_numbers[t], t.e, t.angle) for t in angle_types_used]))

try:

if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d\t%f\t%f\t%f\t%f" % ((dihedral_type_numbers[t],)+t.e) for t in dihedral_types_used]))

except:

print t

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in [a.index, 1, atom_type_numbers[a.type], a.charge, a.x, a.y, a.z]] ) for a in atoms]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, bond_type_numbers[bond_types[i]], b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, angle_type_numbers[angle_types[i]]]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, dihedral_type_numbers[dihedral_types[i]]]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

f.close()

dihedrals = [d for d in dihedrals if any(d.type.e)]

if not atom_types:

atom_types = dict( [(t.type,True) for t in atoms] ).keys() #unique set of atom types

bond_types = dict( [(t.type,True) for t in bonds] ).keys()

angle_types = dict( [(t.type,True) for t in angles] ).keys()

dihedral_types = dict( [(t.type,True) for t in dihedrals] ).keys()

atom_type_numbers = dict( [(t,i+1) for i,t in enumerate(atom_types)] ) #assign unique numbers

bond_type_numbers = dict( [(t,i+1) for i,t in enumerate(bond_types)] )

angle_type_numbers = dict( [(t,i+1) for i,t in enumerate(angle_types)] )

dihedral_type_numbers = dict( [(t,i+1) for i,t in enumerate(dihedral_types)] )

f = open(run_name+'.data', 'w')

f.write('LAMMPS Description\n\n%d atoms\n%d bonds\n%d angles\n%d dihedrals\n0 impropers\n\n' % (len(atoms), len(bonds), len(angles), len(dihedrals)) )

f.write('%d atom types\n%d bond types\n%d angle types\n%d dihedral types\n0 improper types\n' % (len(atom_types), len(bond_types), len(angle_types), len(dihedral_types)) )

f.write('''

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom_type_numbers[t], t.mass) for t in atom_types]))+'\n')

if pair_coeffs_included: f.write('\nPair Coeffs\n\n'+('\n'.join(["%d\t%f\t%f" % (atom_type_numbers[t], t.vdw_e, t.vdw_r) for t in atom_types])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (bond_type_numbers[t], t.e, t.r) for t in bond_types]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (angle_type_numbers[t], t.e, t.angle) for t in angle_types]))

if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d\t%f\t%f\t%f\t%f" % ((dihedral_type_numbers[t],)+tuple(t.e)+((0.0,) if len(t.e)==3 else ()) ) for t in dihedral_types]))

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in [a.index, 1, atom_type_numbers[a.type], a.charge, a.x, a.y, a.z]] ) for a in atoms]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, bond_type_numbers[b.type], b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, angle_type_numbers[a.type]]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, dihedral_type_numbers[d.type]]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

box_size = (100,100,100)

os.chdir('lammps')

f = open(run_name+'.data', 'w')

f.write('''LAMMPS Description

'''+str(len(atoms))+''' atoms

'''+str(len(bonds))+''' bonds

'''+str(len(angles))+''' angles

'''+str(len(dihedrals))+''' dihedrals

0 impropers

'''+str(len(atoms))+''' atom types

'''+str(len(bonds))+''' bond types

'''+str(len(angles))+''' angle types

'''+str(len(dihedrals))+''' dihedral types

0 improper types

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom.index, atom.type.mass) for atom in atoms]))+'''

Pair Coeffs

'''+('\n'.join(["%d\t%f\t%f" % (atom.index, atom.type.vdw_e, atom.type.vdw_r) for atom in atoms])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, bond.e, bond.d) for i,bond in enumerate(bonds)]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, angle.e, angle.theta) for i,angle in enumerate(angles)]))

if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d\t%f\t%f\t%f\t%f" % ((i+1,)+tuple(dihedral.e)) for i,dihedral in enumerate(dihedrals) ]))

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in (a.index, 1, a.index, a.charge, a.x, a.y, a.z)] ) for i,a in enumerate(atoms) ]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1, b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

f.close()

steps = 1000

T = 94

P = 1.5

os.chdir('lammps')

f = open(run_name+".in", 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

'''+("newton off\npackage gpu force/neigh 0 1 1" if run_on == 'gpu' else "")+'''

#pair_style lj/cut/coul/long'''+("/gpu" if run_on == 'gpu' else "")+''' 10.0 8.0

pair_style lj/cut/coul/cut 10.0 8.0

bond_style harmonic

angle_style harmonic

dihedral_style opls

#kspace_style pppm 1.0e-6

special_bonds lj/coul 0.0 0.0 0.5

read_data '''+run_name+'''.data

thermo_style custom temp press vol pe etotal tpcpu

thermo 300#'''+str(max(100,steps/100))+'''

#dump 1 all xyz '''+str(max(10,steps/1000))+''' '''+run_name+'''.xyz

dump 1 all xyz 100 '''+run_name+'''.xyz

minimize 0.0 1.0e-8 1000 100000

velocity all create 5000 1 rot yes dist gaussian

timestep 1.0

fix anneal all nvt temp 5000 1 10

print "anneal"

run 30000

unfix anneal

minimize 0.0 1.0e-8 1000 100000

#velocity all create '''+str(T)+''' 1 rot yes dist gaussian

#timestep 2.0

#fix pressurize all npt temp '''+str(T)+''' '''+str(T)+''' 10 iso '''+str(P)+" "+str(P)+''' 100

#print "Pressurize"

#run 3000

#unfix pressurize

#velocity all create '''+str(T)+''' 1 rot yes dist gaussian

#timestep 2.0

#fix 1 all nvt temp '''+str(T)+" "+str(T)+''' 100

#print "Running"

#run '''+str(steps))

f.close()

if run_on == 'cluster':

f = open(run_name+".nbs", 'w')

f.write('''#!/bin/bash

##NBS-nproc: 4

##NBS-speed: 3000

##NBS-queue: "batch"

$NBS_PATH/mpiexec /fs/home/jms875/bin/lammps -in %s.in > %s.log

''' % (run_name, run_name) )

f.close()

os.system("jsub "+run_name+".nbs")

elif run_on == 'gpu':

f = open(run_name+".nbs", 'w')

f.write('''#!/bin/bash

##NBS-nproc: 2

##NBS-queue: "gpudev"

export PATH="$PATH:/opt/nvidia/cuda/bin"

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/nvidia/cuda/lib64"

$NBS_PATH/mpiexec /fs/home/jms875/bin/lammps_gpu -in %s.in > %s.log

''' % (run_name, run_name) )

f.close()

os.system("jsub "+run_name+".nbs")

else:

if os.system("lammps < "+run_name+".in") == 0:

pass#os.system("python view.py "+run_name)

os.chdir('lammps')

f = open(run_name+".in", 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

#pair_style lj/cut/coul/long 10.0 8.0

pair_style lj/cut/coul/cut 10.0 8.0

bond_style harmonic

angle_style harmonic

dihedral_style opls

#kspace_style pppm 1.0e-6

special_bonds lj/coul 0.0 0.0 0.5

read_data '''+run_name+'''.data

'''+('fix holdit all restrain '+( {2:'bond',3:'angle',4:'dihedral'}[len(restrained.atoms)] )+' '+' '.join([str(a.index) for a in restrained.atoms])+' 2000.0 2000.0 '+str(restraint_value) if restrained else '')+'''

thermo_style custom pe

dump 1 all xyz 1000 '''+run_name+'''.xyz

fix_modify holdit energy yes

minimize 0.0 1.0e-8 1000 100000\n\n''')

f.close()

if os.system("lammps < "+run_name+".in") != 0:

raise Exception('Minimize failed')

run_name = utils.unique_filename('lammps/', 'anneal_'+name, '.data')

write_data_file(atoms, bonds, angles, dihedrals, params, run_name)

run_anneal(run_name)

jsub.wait(run_name)

tail = subprocess.Popen('tail lammps/'+run_name+'.xyz -n '+str(len(atoms)), shell=True, stdout=subprocess.PIPE).communicate()[0]

if 'No such file or directory' in tail:

raise Exception('Anneal '+run_name+' failed')

for i,line in enumerate(tail.splitlines()):

atoms[i].x, atoms[i].y, atoms[i].z = [float(s) for s in line.split()[1:]]

run_name = utils.unique_filename('lammps/', 'minimize_'+name, '.data')

write_data_file(atoms, bonds, angles, dihedrals, params, run_name)

run_minimize(run_name, restrained=restrained, restraint_value=restraint_value)

tail = subprocess.Popen('tail lammps/'+run_name+'.xyz -n '+str(len(atoms)), shell=True, stdout=subprocess.PIPE).communicate()[0]

if not tail:

raise Exception('Minimize failed')

run_name = utils.unique_filename('lammps/', 'minimize2_'+name, '.data')

write_data_file2(atoms, bonds, angles, dihedrals, run_name)

run_minimize(run_name, restrained=restrained, restraint_value=restraint_value)

tail = subprocess.Popen('tail lammps/'+run_name+'.xyz -n '+str(len(atoms)), shell=True, stdout=subprocess.PIPE).communicate()[0]

if not tail:

raise Exception('Minimize failed')

run_name = 'dihedral_values'

write_data_file2(atoms, bonds, angles, dihedrals, run_name)

os.chdir('lammps')

f = open(run_name+'.in', 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

pair_style lj/cut/coul/cut 10.0

bond_style harmonic

angle_style harmonic

dihedral_style opls

read_data '''+run_name+'''.data

compute 1 all dihedral/local phi

compute 2 all property/local dtype

dump d1 all local 1000 '''+run_name+'''.dat c_1 c_2

run 0

''')

f.close()

#if subprocess.call('lammps < '+run_name+'.in', shell=True) != 0:

# raise Exception('Getting dihedral values failed')

result = subprocess.Popen('lammps < '+run_name+'.in', shell=True, stdout=subprocess.PIPE).communicate()[0]

pairs = [ (int(line.split()[1]), float(line.split()[0])) for line in open(run_name+'.dat').readlines()[-len(dihedrals):] ]

os.chdir('..')

#print pairs

box_size = (100,100,100)

os.chdir('lammps')

f = open('internal_coords.data', 'w')

f.write('''LAMMPS Description

'''+str(len(atoms))+''' atoms

'''+str(len(bonds))+''' bonds

'''+str(len(angles))+''' angles

'''+str(len(dihedrals)*0)+''' dihedrals

0 impropers

'''+str(len(atoms))+''' atom types

'''+str(len(bonds))+''' bond types

'''+str(len(angles))+''' angle types

'''+str(len(dihedrals)*0)+''' dihedral types

0 improper types

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom.index, atom.type.mass) for atom in atoms]))+'''

Pair Coeffs

'''+('\n'.join(["%d\t%f\t%f" % (atom.index, atom.type.vdw_e, atom.type.vdw_r) for atom in atoms])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, max(10, bond.e), bond.d) for i,bond in enumerate(bonds)]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, max(10, angle.e), angle.theta) for i,angle in enumerate(angles)]))

#if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d 10 1 %d 0.5" % (i+1, dihedral.theta+180) for i,dihedral in enumerate(dihedrals) ])) #energy 1 angle(degrees) weighting

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in (a.index, 1, a.index, a.charge, a.x, a.y, a.z)] ) for i,a in enumerate(atoms) ]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1, b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

#if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

f.close()

#'''+ '\n'.join(['fix dih'+str(i)+' all restrain dihedral '+' '.join([str(a.index) for a in d.atoms])+(' 0.0 0.0 ' if d!=strong_dihedral else ' 0.0 0.0 ')+str(d.theta+180)+'\nfix_modify dih'+str(i)+' energy yes' for i,d in enumerate(dihedrals)]) +'''

f = open('internal_coords.in', 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

pair_style lj/cut/coul/cut 10.0 8.0 #0.01 0.01

#pair_style lj/charmm/coul/charmm 8.0 10.0

bond_style harmonic

angle_style harmonic

#dihedral_style charmm

special_bonds lj/coul 0.0 0.0 0.5

read_data internal_coords.data

thermo_style custom epair emol etotal

dump 1 all xyz 1 internal_coords.xyz

#minimize 0.0 1.0e-8 1000 100000

#velocity all create 600.0 1337 mom yes rot yes dist gaussian

#fix NVE all nve/limit 1.0

#fix TFIX all langevin 600.0 0.0 100 1337

#run 10000

#fix TFIX all langevin 0.0 0.0 100 24601

#run 10000

minimize 0.0 1.0e-8 1000 100000

''')

f.close()

if subprocess.call('lammps < internal_coords.in', shell=True) != 0:

raise Exception('Setting internal coordinates failed')

tail = subprocess.Popen('tail internal_coords.xyz -n '+str(len(atoms)), shell=True, stdout=subprocess.PIPE).communicate()[0]

os.chdir('..')

box_size = (100,100,100)

os.chdir('lammps')

f = open('energy.data', 'w')

f.write('''LAMMPS Description

'''+str(len(atoms))+''' atoms

'''+str(len(bonds))+''' bonds

'''+str(len(angles))+''' angles

'''+str(len(dihedrals))+''' dihedrals

0 impropers

'''+str(len(atoms))+''' atom types

'''+str(len(bonds))+''' bond types

'''+str(len(angles))+''' angle types

'''+str(len(dihedrals))+''' dihedral types

0 improper types

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom.index, atom.type.mass) for atom in atoms]))+'''

Pair Coeffs

'''+('\n'.join(["%d\t%f\t%f" % (atom.index, atom.type.vdw_e, atom.type.vdw_r) for atom in atoms])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, params.bond_e[i], bond.d) for i,bond in enumerate(bonds)]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, params.angle_e[i], angle.theta) for i,angle in enumerate(angles)]))

if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d\t%f\t%f\t%f\t%f" % ((i+1,)+tuple(params.dihedral_e[i])) for i,dihedral in enumerate(dihedrals) ]))

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in (a.index, 1, a.index, a.charge)+tuple(coords[i])] ) for i,a in enumerate(atoms) ]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1, b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

f.close()

f = open('energy.in', 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

#pair_style lj/cut/coul/long 10.0 8.0

pair_style lj/cut/coul/cut 10.0 8.0

bond_style harmonic

angle_style harmonic

dihedral_style opls

#kspace_style pppm 1.0e-6

special_bonds lj/coul 0.0 0.0 0.5

read_data energy.data

thermo_style custom etotal

run 0

''')

f.close()

result = subprocess.Popen('lammps < energy.in', shell=True, stdout=subprocess.PIPE).communicate()[0]

energy = float( re.search('TotEng\s+(\S+)', result).group(1) )

os.chdir('..')

run_name = 'energy'

directory = 'lammps'

box_size = (100,)*3

starting_coords = [(a.x, a.y, a.z) for a in atoms]

for i,a in enumerate(atoms):

a.x, a.y, a.z = coords[i]

atom_types = dict( [(t.type,True) for t in atoms] ).keys()

hbonded = False

polar_H_label = [a.type.index+1 for i,a in enumerate(atoms) if a.element=='H' and a.charge>0.3][0]

electron_donor_type = [a.type for i,a in enumerate(atoms) if a.element=='N' and a.charge<-0.5][0]

is_charged = any([a.charge!=0.0 for a in atoms])

if not os.path.isdir(directory):

os.mkdir(directory)

os.chdir(directory)

if hbonded:

write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name, pair_coeffs_included=False)

else:

write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name)

f = open(run_name+'.in', 'w')

f.write('''units real\natom_style full #bonds, angles, dihedrals, impropers, charges\n''')

if hbonded:

f.write('pair_style hybrid/overlay hbond/dreiding/morse 2 9.0 11.0 90 lj/cut/coul/cut 20.0\n')

elif is_charged:

f.write('pair_style lj/cut/coul/cut 20.0\n')

else:

f.write('pair_style lj/cut 10.0\n')

if bonds: f.write('bond_style harmonic\n')

if angles: f.write('angle_style harmonic\n')

if dihedrals: f.write('dihedral_style opls\n')

f.write('''special_bonds lj/coul 0.0 0.0 0.5\nread_data '''+run_name+'''.data\n''')

if hbonded:

for ii,a in enumerate(atom_types):

for jj,b in enumerate(atom_types[ii:]):

i = ii+1; j = i+jj

vdw_e = (a.vdw_e * b.vdw_e)**0.5

vdw_r = (a.vdw_r * b.vdw_r)**0.5

f.write('pair_coeff %d %d lj/cut/coul/cut %f %f\n' % (i, j, vdw_e, vdw_r))

if a==electron_donor_type and b==electron_donor_type:

#http://pubs.acs.org/doi/suppl/10.1021/ja8100227 supplementary materials

D0 = 0.4300

r0 = 3.4000

alpha = 5/r0

for donor_flag in ['i','j']: #donor = electronegative atom bonded to the H

f.write('pair_coeff %d %d hbond/dreiding/morse %d %s %f %f %f 2\n' % (i, j, polar_H_label, donor_flag, D0, alpha, r0))

f.write('''

compute hb all pair hbond/dreiding/morse

variable C_hbond equal c_hb[1] #number hbonds

variable E_hbond equal c_hb[2] #hbond energy

thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond

''')

f.write('''

thermo_modify line multi format float %14.6f

run 0

''')

f.close()

#os.system('lammps < '+run_name+'.in')

#sys.exit(0)

result = subprocess.Popen('lammps < '+run_name+'.in', shell=True, stdout=subprocess.PIPE).communicate()[0]

energy = float( re.search('TotEng\s+=\s+(\S+)', result).group(1) )

os.chdir('..')

for i,a in enumerate(atoms):

a.x, a.y, a.z = starting_coords[i]

run_name = 'minimize_rigid'

directory = 'lammps'

box_size = (100,)*3

atom_types = dict( [(t.type,True) for t in atoms] ).keys()

os.chdir(directory)

write_data_file_general(atoms, [], [], [], box_size, run_name)

f = open(run_name+'.in', 'w')

f.write('''units real\natom_style full #bonds, angles, dihedrals, impropers, charges\n''')

f.write('pair_style lj/cut/coul/cut 20.0\n')

f.write('''special_bonds lj/coul 0.0 0.0 0.0\nread_data '''+run_name+'''.data\n''')

f.write('''thermo_style custom etotal evdwl ecoul

thermo_modify line multi format float %14.6f

thermo 10000

dump 1 all xyz 10000 '''+run_name+'''.xyz

timestep 0.01\n''')

for g in rigid_groups:

f.write('group g%d id %d:%d\n' % (g[0],g[0],g[1]) )

f.write('fix move all rigid/nvt group '+str(len(rigid_groups))+' '+(' '.join(['g'+str(g[0]) for g in rigid_groups]))+' temp 90.0 90.0 5.0\nrun 10000\n')

f.close()

#os.system('lammps < '+run_name+'.in')

#sys.exit(0)

result = subprocess.Popen('lammps < '+run_name+'.in', shell=True, stdout=subprocess.PIPE).communicate()[0]

total_energy = float( re.search('TotEng\s+=\s+(\S+)', result).group(1) )

coul_energy = float( re.search('E_coul\s+=\s+(\S+)', result).group(1) )

for i,line in enumerate([line for line in open(run_name+'.xyz').readlines() if len(line.split())==4][-len(atoms):]):

columns = line.split()

atoms[i].x, atoms[i].y, atoms[i].z = [float(x) for x in columns[1:]]

os.chdir('..')

run_name = utils.unique_filename('lammps/', 'eval', '.data')

import copy

atoms = []

bonds = []

angles = []

dihedrals = []

for mol in range(N):

for a in mol_atoms:

aa = copy.copy(a)

aa.y += mol*10.

aa.index += mol*len(mol_atoms)

atoms.append(aa)

for b in mol_bonds:

bb = copy.copy(b)

bb.atoms = [atoms[ x.index-1+mol*len(mol_atoms) ] for x in b.atoms]

bonds.append(bb)

for b in mol_angles:

bb = copy.copy(b)

bb.atoms = [atoms[ x.index-1+mol*len(mol_atoms) ] for x in b.atoms]

angles.append(bb)

for b in mol_dihedrals:

bb = copy.copy(b)

bb.atoms = [atoms[ x.index-1+mol*len(mol_atoms) ] for x in b.atoms]

dihedrals.append(bb)

box_size = (max(atoms, key=lambda a: a.x).x*2+100, max(atoms, key=lambda a: a.y).y*2+100, max(atoms, key=lambda a: a.z).z*2+100)

os.chdir('lammps')

f = open(run_name+'.data', 'w')

f.write('''LAMMPS Description

'''+str(len(atoms))+''' atoms

'''+str(len(bonds))+''' bonds

'''+str(len(angles))+''' angles

'''+str(len(dihedrals))+''' dihedrals

0 impropers

'''+str(len(atoms))+''' atom types

'''+str(len(bonds))+''' bond types

'''+str(len(angles))+''' angle types

'''+str(len(dihedrals))+''' dihedral types

0 improper types

-'''+str(box_size[0]/2)+''' '''+str(box_size[0]/2)+''' xlo xhi

-'''+str(box_size[1]/2)+''' '''+str(box_size[1]/2)+''' ylo yhi

-'''+str(box_size[2]/2)+''' '''+str(box_size[2]/2)+''' zlo zhi

Masses

'''+('\n'.join(["%d\t%f" % (atom.index, atom.type.mass) for atom in atoms]))+'''

Pair Coeffs

'''+('\n'.join(["%d\t%f\t%f" % (atom.index, atom.type.vdw_e, atom.type.vdw_r) for atom in atoms])) )

if bonds: f.write("\n\nBond Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, bond.e, bond.d) for i,bond in enumerate(bonds)]))

if angles: f.write("\n\nAngle Coeffs\n\n"+'\n'.join(["%d\t%f\t%f" % (i+1, angle.e, angle.theta) for i,angle in enumerate(angles)]))

if dihedrals: f.write("\n\nDihedral Coeffs\n\n"+'\n'.join(["%d\t%f\t%f\t%f\t%f" % ((i+1,)+tuple(dihedral.e)) for i,dihedral in enumerate(dihedrals) ]))

f.write("\n\nAtoms\n\n"+'\n'.join( ['\t'.join( [str(q) for q in (a.index, 1, a.index, a.charge, a.x, a.y, a.z)] ) for i,a in enumerate(atoms) ]) ) #atom (molecule type charge x y z)

if bonds: f.write('\n\nBonds\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1, b.atoms[0].index, b.atoms[1].index]]) for i,b in enumerate(bonds)]) ) #bond (type a b)

if angles: f.write('\n\nAngles\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in a.atoms] ]) for i,a in enumerate(angles)]) ) #ID type atom1 atom2 atom3

if dihedrals: f.write('\n\nDihedrals\n\n' + '\n'.join( ['\t'.join([str(q) for q in [i+1, i+1]+[atom.index for atom in d.atoms] ]) for i,d in enumerate(dihedrals)]) ) #ID type a b c d

f.write('\n\n')

f.close()

f = open(run_name+'.in', 'w')

f.write('''units real

atom_style full #bonds, angles, dihedrals, impropers, charges

#pair_style lj/cut/coul/long 10.0 8.0

pair_style lj/cut/coul/cut 10.0 8.0

bond_style harmonic

angle_style harmonic

dihedral_style opls

#kspace_style pppm 1.0e-6

special_bonds lj/coul 0.0 0.0 0.5

read_data '''+run_name+'''.data

thermo_style custom temp press vol pe etotal tpcpu

thermo 300

dump 1 all xyz 100 '''+run_name+'''.xyz

minimize 0.0 1.0e-8 1000 100000

velocity all create 5000 1 rot yes dist gaussian

timestep 1.0

fix anneal all nvt temp 5000 1 10

print "anneal"

run 30000

unfix anneal

minimize 0.0 1.0e-8 1000 100000

''')

f.close()

os.system('lammps < '+run_name+'.in')