def compare_distances_only():
utils.Molecule.set_params('oplsaa4.prm')
for f in [
'propanenitrile', 'butanenitrile', 'pentanenitrile',
'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2',
'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2',
'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2'
]:
atoms0 = utils.Molecule(f + '.arc').atoms
atoms1 = gaussian.parse_atoms('gaussian/' + f + '_1.log')[1]
for i in range(len(atoms0)):
atoms0[i].index = i + 1
atoms1[i].index = i + 1
#atoms0[i].x = atoms1[i].xp
#atoms0[i].y = atoms1[i].y
#atoms0[i].z = atoms1[i].z
bonds0 = filetypes.get_bonds(atoms0)
bonds1 = filetypes.get_bonds(atoms1)
#filetypes.write_arc(f[:-1]+'3', atoms0)
#continue
angles0, dihedrals0 = filetypes.get_angles_and_dihedrals(
atoms0, bonds0)
angles1, dihedrals1 = filetypes.get_angles_and_dihedrals(
atoms1, bonds1)
bond_error = 0.0
for i in range(len(bonds0)):
bond_error += abs(bonds0[i].d - bonds1[i].d)
angles0.sort(key=lambda a: tuple([n.index for n in a.atoms]))
angles1.sort(key=lambda a: tuple([n.index for n in a.atoms]))
angle_error = 0.0
for i in range(len(angles0)):
d0 = utils.dist(angles0[i].atoms[0], angles0[i].atoms[2])
d1 = utils.dist(angles1[i].atoms[0], angles1[i].atoms[2])
angle_error += abs(d0 - d1)
dihedrals0.sort(key=lambda a: tuple([n.index for n in a.atoms]))
dihedrals1.sort(key=lambda a: tuple([n.index for n in a.atoms]))
if dihedrals0:
dihedral_error = 0.0
for i in range(len(dihedrals0)):
#if dihedral is single-bonded free rotor, ignore comparison
if (dihedrals0[i].atoms[1].type.index,
dihedrals0[i].atoms[1].type.index) == (78, 78):
continue
d0 = utils.dist(dihedrals0[i].atoms[0], dihedrals0[i].atoms[3])
d1 = utils.dist(dihedrals1[i].atoms[0], dihedrals1[i].atoms[3])
dihedral_error += abs(d0 - d1)
print f, bond_error / len(bonds0), angle_error / len(
angles0), 180 / math.pi * dihedral_error / len(dihedrals0)
else:
print f, bond_error / len(bonds0), angle_error / len(angles0), 0.0
def minimize():
#for f in ['propanenitrile', 'butanenitrile', 'pentanenitrile', 'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2', 'aminohexane2', 'hexane2', 'methane']:
for f in [
'hcn34', 'cyanoacetylene34', 'acrylonitrile34', 'cyanoallene34',
'acetonitrile34', 'hc5n34'
]:
atoms = utils.Molecule(f + '.arc').atoms
gaussian.job(atoms,
'M062X/aug-cc-pVDZ',
'batch',
f + '_0',
'Opt',
procs=1)
gaussian.job(atoms,
'M062X/aug-cc-pVDZ',
'batch',
f + '_1',
'Opt SCRF(Solvent=n-Hexane)',
procs=1)
def run(test_molecule_filename, makefile):
utils.Molecule.set_params('../micelle/oplsaa4.prm')
test_molecule = utils.Molecule(test_molecule_filename)
test_molecule_name = test_molecule_filename[test_molecule_filename.
rindex('/') + 1:-4]
if test_molecule_name[-1] == '2':
test_molecule_name = test_molecule_name[:-1]
solvent = copy.deepcopy(test_molecule)
solvent_spacing = [(max(solvent.atoms, key=lambda a: a.x).x -
min(solvent.atoms, key=lambda a: a.x).x),
(max(solvent.atoms, key=lambda a: a.y).y -
min(solvent.atoms, key=lambda a: a.y).y),
(max(solvent.atoms, key=lambda a: a.z).z -
min(solvent.atoms, key=lambda a: a.z).z)]
solvent_spacing = [x + 1.0 for x in solvent_spacing]
max_vdw_r = max(solvent.atoms, key=lambda a: a.type.vdw_r).type.vdw_r
solvent_spacing = [max(x, max_vdw_r) for x in solvent_spacing]
if test_molecule_name == 'propanenitrile' or test_molecule_name == 'acetonitrile':
solvent_spacing[2] += 1.0
if test_molecule_name == 'hcn':
solvent_spacing[0] += 0.5
if test_molecule_name == 'acetylene':
pass
L = 6
box_size = [L * x for x in solvent_spacing]
atoms = []
bonds = []
angles = []
dihedrals = []
#add staggering between layers (like shingles)
for xi in range(L):
for yi in range(L):
for zi in range(L):
x = xi * solvent_spacing[0] - box_size[0] / 2
y = yi * solvent_spacing[1] - box_size[1] / 2
z = (zi + xi * 0.5) * solvent_spacing[2] - box_size[2] / 2
if xi == 0 and yi == 0 and zi == 0:
test_molecule.add_to(x, y, z, atoms, bonds, angles,
dihedrals)
else:
if True: #(xi+yi+zi)%2==0:
solvent.add_to(x, y, z, atoms, bonds, angles,
dihedrals)
else:
for a in solvent.atoms:
a.z = -a.z
solvent.add_to(x, y, z, atoms, bonds, angles,
dihedrals)
for a in solvent.atoms:
a.z = -a.z
T = 94.0
P = 1.45
#filetypes.write_xyz('out', atoms)
#sys.exit()
os.chdir('lammps')
original_vdw_e = [a.type.vdw_e for a in test_molecule.atoms]
original_charges = [a.type.charge for a in test_molecule.atoms]
n_steps = 100
for step in range(0, n_steps + 1):
for i, x in enumerate(test_molecule.atoms):
a = atoms[i]
a.type.vdw_e = original_vdw_e[i] * (
1.0 * step / n_steps)**2 #since LJ eps is geometric mean
a.type.charge = original_charges[i] * step / n_steps
a.charge = a.type.charge
run_name = test_molecule_name + '_solid2__' + str(int(step))
atom_types = dict([(t.type, True) for t in atoms]).keys()
atom_type_numbers = dict([(t, i + 1)
for i, t in enumerate(atom_types)])
is_charged = any([a.charge != 0.0 for a in atoms])
lammps.write_data_file_general(atoms,
bonds,
angles,
dihedrals,
box_size,
run_name,
atom_types=atom_types)
pickle.dump((atoms, bonds, angles, dihedrals),
open(run_name + '.pickle', 'w'))
os.system('cp ../' + sys.argv[0] + ' ' + run_name + '.py')
f = open(run_name + '.in', 'w')
f.write(
'units real\natom_style full #bonds, angles, dihedrals, impropers, charges\n'
)
if is_charged:
f.write('pair_style lj/cut/coul/long 8.0\n')
else:
f.write('pair_style lj/cut 8.0\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')
if is_charged: f.write('kspace_style pppm 1.0e-3\n')
f.write('special_bonds lj/coul 0.0 0.0 0.5\nread_data ' + run_name +
'.data\n')
test_molecule_types = dict([
(t.type, True) for t in atoms[:len(test_molecule.atoms)]
]).keys()
f.write('''thermo 0
dump 1 all xyz 10000 ''' + run_name + '''.xyz
group test_molecule id <= ''' + str(len(test_molecule.atoms)) + '''
group others subtract all test_molecule
compute SolEng test_molecule group/group others
thermo_style custom c_SolEng
#thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_SolEng tpcpu
#thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
fix relax all nve/limit 0.01
fix drag all viscous 0.05
timestep 2.0
run 2500
unfix relax
fix relax all nve
run 25000
unfix relax
unfix drag
velocity all create ''' + str(T) + ''' 1 rot yes dist gaussian
fix press all npt temp ''' + str(T) + ' ' + str(T) + ''' 100 aniso ''' +
str(P) + ' ' + str(P) + ''' 1000
timestep 2.0
thermo 1
run 250000
''')
f.close()
if True: #start multiple processes
#os.system('nohup ~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
makefile.write(
'%s:\n\t~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null\n'
% (run_name, run_name, run_name))
print 'Running', run_name
else:
os.system('~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log' %
(run_name, run_name))
sys.exit()
os.chdir('..')
def run(filename):
tail = utils.Molecule(filename + '.arc')
atoms = []
bonds = []
angles = []
dihedrals = []
tail.add_to(0., 0., 0., atoms, bonds, angles, dihedrals)
box_size = [40.] * 3
T = 100.0
directory = 'lammps'
if not os.path.isdir(directory):
os.mkdir(directory)
os.chdir(directory)
run_name = 'opls_' + filename
atom_types = dict([(t.type, True) for t in atoms]).keys()
atom_type_numbers = dict([(t, i + 1) for i, t in enumerate(atom_types)])
is_charged = any([a.charge != 0.0 for a in atoms])
lammps.write_data_file_general(atoms,
bonds,
angles,
dihedrals,
box_size,
run_name,
atom_types=atom_types)
os.system('cp ../' + sys.argv[0] + ' ' + run_name + '.py')
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/long 8.0\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('kspace_style pppm 1.0e-3\n')
f.write('''special_bonds lj/coul 0.0 0.0 0.5
read_data ''' + run_name + '''.data\n
dump 1 all xyz 250000 ''' + run_name + '''.xyz
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
group mobile id > 1
velocity mobile create ''' + str(T) + ''' 1
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
fix anneal mobile nvt temp ''' + str(T) + ''' 1.0 50.0
timestep 4.0
run 250000
minimize 0.0 1.0e-8 1000 100000
''')
f.close()
os.system('lammps -in ' + run_name + '.in -log ' + run_name + '.log')
os.chdir('..')
def run(test_molecule_filename, solvent_ratio=[100,0,0]):
utils.Molecule.set_params('../micelle/oplsaa4.prm')
test_molecule = utils.Molecule(test_molecule_filename)
test_molecule_name = test_molecule_filename[ test_molecule_filename.rindex('/')+1 :-4]
if test_molecule_name[-2:] in ['e2','n2']: test_molecule_name = test_molecule_name[:-1]
N2 = utils.Molecule('../N2.arc')
#N2 params: http://www.sciencedirect.com/science/article/pii/002240739290142Q
N2.atoms[0].type.vdw_r = 3.35
N2.atoms[0].type.vdw_e = 0.0721
#http://cccbdb.nist.gov/exp2.asp?casno=7727379
N2.bonds[0].type.r = 1.0977
solvents = [utils.Molecule('../micelle/methane.arc'), utils.Molecule('../ethane.arc'), copy.deepcopy(N2)]
water_types = []
atoms = []
bonds = []
angles = []
dihedrals = []
test_molecule.add_to(0.0, 0.0, 0.0, atoms, bonds, angles, dihedrals)
box_size = (20,20,20)
atom_count = len(atoms)
solvent_amount_to_add = [ratio for ratio in solvent_ratio]
solvent = solvents[0] #cheesy
solvent_spacing = [(max(solvent.atoms, key=lambda a:a.x).x-min(solvent.atoms, key=lambda a:a.x).x), (max(solvent.atoms, key=lambda a:a.y).y-min(solvent.atoms, key=lambda a:a.y).y), (max(solvent.atoms, key=lambda a:a.z).z-min(solvent.atoms, key=lambda a:a.z).z)]
max_vdw_r = max(solvent.atoms, key=lambda a:a.type.vdw_r).type.vdw_r
solvent_spacing = [max(x,max_vdw_r) for x in solvent_spacing]
for x in range(-box_size[0]/2+solvent_spacing[0], box_size[0]/2, solvent_spacing[0]):
for y in range(-box_size[1]/2+solvent_spacing[1], box_size[1]/2, solvent_spacing[1]):
for z in range(-box_size[2]/2+solvent_spacing[2], box_size[2]/2, solvent_spacing[2]):
try:
for a in atoms[:atom_count]:
if (a.x-x)**2 + (a.y-y)**2 + (a.z-z)**2 < max_vdw_r**2:
raise AssertionError()
while True:
index_to_add = random.randrange(len(solvents))
if solvent_amount_to_add[ index_to_add ] > 0:
solvents[ index_to_add ].add_to(x, y, z, atoms, bonds, angles, dihedrals)
solvent_amount_to_add[ index_to_add ] -= 1
if sum(solvent_amount_to_add) == 0:
solvent_amount_to_add = [ratio for ratio in solvent_ratio]
break
except AssertionError: pass
T = 94.0
P = 1.45
filetypes.write_xyz('out', atoms)
os.chdir('lammps')
original_vdw_e = [a.type.vdw_e for a in test_molecule.atoms]
original_charges = [a.type.charge for a in test_molecule.atoms]
n_steps = 100
for step in range(0,n_steps+1):
for i,x in enumerate(test_molecule.atoms):
a = atoms[i]
a.type.vdw_e = original_vdw_e[i] * (1.0*step/n_steps)**2 #since LJ eps is geometric mean
a.type.charge = original_charges[i] * step/n_steps
a.charge = a.type.charge
run_name = test_molecule_name+'_'+('_'.join([str(x) for x in solvent_ratio]))+'__'+str(int(step))
atom_types = dict( [(t.type,True) for t in atoms] ).keys()
atom_type_numbers = dict( [(t,i+1) for i,t in enumerate(atom_types)] )
is_charged = any([a.charge!=0.0 for a in atoms])
lammps.write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name, atom_types=atom_types)
pickle.dump((atoms, bonds, angles, dihedrals), open(run_name+'.pickle', 'w'))
os.system('cp ../'+sys.argv[0]+' '+run_name+'.py')
f = open(run_name+'.in', 'w')
f.write('units real\natom_style full #bonds, angles, dihedrals, impropers, charges\n')
if is_charged:
f.write('pair_style lj/cut/coul/long 8.0\n')
else:
f.write('pair_style lj/cut 8.0\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')
if is_charged: f.write('kspace_style pppm 1.0e-3\n')
f.write('special_bonds lj/coul 0.0 0.0 0.5\nread_data '+run_name+'.data\n')
test_molecule_types = dict( [(t.type,True) for t in atoms[:len(test_molecule.atoms)]] ).keys()
f.write('''thermo 0
dump 1 all xyz 10000 '''+run_name+'''.xyz
group test_molecule id <= '''+str(len(test_molecule.atoms))+'''
group others subtract all test_molecule
compute SolEng test_molecule group/group others
thermo_style custom c_SolEng
#thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_SolEng tpcpu
#thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000\n''')
if water_types: #rigid water model
f.write(('fix rigid_water all shake 0.0001 20 0 t'+(' %d'*len(water_types))+'\n') % tuple([atom_type_numbers[t] for t in water_types]) )
f.write('''
velocity all create '''+str(T)+''' 1 rot yes dist gaussian
fix press all npt temp '''+str(T)+' '+str(T)+''' 100 iso '''+str(P)+' '+str(P)+''' 1000
timestep 2.0
thermo 1
run 250000
''')
f.close()
if True: #start multiple processes
#os.system('nohup ~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
makefile.write( '%s:\n\t~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null\n' % (run_name, run_name, run_name) )
print 'Running', run_name
else:
os.system('~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
def compare():
utils.Molecule.set_params('oplsaa4.prm')
for f in [
'propanenitrile', 'butanenitrile', 'pentanenitrile',
'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2',
'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2',
'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2'
]:
atoms0 = utils.Molecule(f + '.arc').atoms
atoms1 = gaussian.parse_atoms('gaussian/' + f + '_0.log')[1]
for i in range(len(atoms0)):
atoms0[i].index = i + 1
atoms1[i].index = i + 1
#atoms0[i].x = atoms1[i].xp
#atoms0[i].y = atoms1[i].y
#atoms0[i].z = atoms1[i].z
bonds0 = filetypes.get_bonds(atoms0)
bonds1 = filetypes.get_bonds(atoms1)
#filetypes.write_arc(f[:-1]+'3', atoms0)
#continue
angles0, dihedrals0 = filetypes.get_angles_and_dihedrals(
atoms0, bonds0)
angles1, dihedrals1 = filetypes.get_angles_and_dihedrals(
atoms1, bonds1)
bond_error = 0.0
for i in range(len(bonds0)):
bond_error += abs(bonds0[i].d - bonds1[i].d)
angles0.sort(key=lambda a: tuple([n.index for n in a.atoms]))
angles1.sort(key=lambda a: tuple([n.index for n in a.atoms]))
angle_error = 0.0
for i in range(len(angles0)):
angle_error += min(
abs(angles0[i].theta - angles1[i].theta),
abs(angles0[i].theta - angles1[i].theta + math.pi * 2),
abs(angles0[i].theta - angles1[i].theta - math.pi * 2))
dihedrals0.sort(key=lambda a: tuple([n.index for n in a.atoms]))
dihedrals1.sort(key=lambda a: tuple([n.index for n in a.atoms]))
angles_by_atoms = {}
for angle in angles1:
angles_by_atoms[tuple(angle.atoms)] = angle
angles_by_atoms[tuple(reversed(angle.atoms))] = angle
if dihedrals0:
dihedral_error = 0.0
for i in range(len(dihedrals0)):
#if dihedral only controls a 180-degree angle, ignore comparison
angle1 = angles_by_atoms[tuple(dihedrals1[i].atoms[1:])]
angle2 = angles_by_atoms[tuple(dihedrals1[i].atoms[:-1])]
#print angle1.theta, angle2.theta,
if abs(angle1.theta -
180) < 2 or abs(angle1.theta + 180) < 2 or abs(
angle2.theta - 180) < 2 or abs(angle2.theta +
180) < 2:
#print angle1.theta, angle2.theta,
continue
#if dihedral is single-bonded free rotor, ignore comparison
if (dihedrals0[i].atoms[1].type.index,
dihedrals0[i].atoms[1].type.index) == (78, 78):
continue
#else make comparison
try:
a, b = utils.dihedral_angle(
*dihedrals0[i].atoms)[0], utils.dihedral_angle(
*dihedrals1[i].atoms)[0]
dihedral_error += min(abs(a - b), abs(a - b + math.pi * 2),
abs(a - b - math.pi * 2))
#print [aa.element for aa in dihedrals0[i].atoms], min( abs(a-b), abs(a-b+math.pi*2), abs(a-b-math.pi*2) )
except ZeroDivisionError:
pass
print f, bond_error / len(bonds0), angle_error / len(
angles0), 180 / math.pi * dihedral_error / len(dihedrals0)
else:
print f, bond_error / len(bonds0), angle_error / len(angles0), 0.0
import os, copy, sys, random, cPickle, math
sys.path.append("/fs/home/jms875/build/lammps/lammps-15May15/python")
from lammps import lammps
sys.path.append("/fs/home/jms875/Library/2.0")
import utils, files
system = utils.System(box_size=(30., 30., 30.), name='test4')
THF = utils.Molecule('cml/THF')
molecules = [THF]
molecule_ratio = [1]
density = 0.889
files.packmol(system, molecules, molecule_ratio, density)
os.chdir('lammps')
files.write_lammps_data(system)
commands = ('''units real
atom_style full
pair_style lj/cut/coul/long 10.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data ''' + system.name + '''.data
kspace_style pppm 1.0e-4
thermo_style custom density tpcpu