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(mode, timescale, step, step_size, makefile):
run_name = 'ti10_'+str(mode)+'__'+str(step)
z_separation = step * step_size
solvent = utils.Molecule('methane.arc')
#solvent = utils.Molecule('benzene2.arc')
#solvent = utils.Molecule('hexane2.arc')
box_size = [21.,21.,42.]
S = 3.5
if mode==3:
tail = utils.Molecule('propanenitrile.arc')
z_offset = -4.5
elif mode==4:
tail = utils.Molecule('butanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.5
elif mode==5:
tail = utils.Molecule('pentanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==6:
tail = utils.Molecule('hexanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==7:
tail = utils.Molecule('aminopropane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 2.5
elif mode==8:
tail = utils.Molecule('aminobutane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, -a.x
z_offset = 3.5
elif mode==9:
tail = utils.Molecule('aminopentane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==10:
tail = utils.Molecule('aminohexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==11:
tail = utils.Molecule('hexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 9.0
elif mode==12:
tail = utils.Molecule('hcn2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
S = 3.0
z_offset = -0.5
elif mode==13:
tail = utils.Molecule('cyanoacetylene2.arc') #unfixed dihedrals irrelevant, since angle=180
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -2.0
elif mode==14:
tail = utils.Molecule('acrylonitrile2.arc') #unfixed dihedrals irrelevant, since angle=180
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
elif mode==15:
tail = utils.Molecule('cyanoallene2.arc') #added one dihedral param (18 19 37 100), other two free, ( 36 37 100 37 ) added too, or modified? Basically, doesn't work in OPLS; allene dihedrals are wrong.
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.0
elif mode==16:
tail = utils.Molecule('acetonitrile2.arc') #all dihedrals free
z_offset = 2.0
elif mode==17:
tail = utils.Molecule('hc5n2.arc') #doesn't work well in OPLS
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
atoms = []
bonds = []
angles = []
dihedrals = []
theta = 0; z = 0.0
molecules_not_added = 0
held_atoms = []
pushed_atoms = []
if mode==11:
for xi in range(box_size[0]/S):
x = xi*S - box_size[0]/2
for yi in range(box_size[1]/S):
y = yi*S - box_size[1]/2
#tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
if xi==3 and yi==3:
tail.add_to(x, y, z+z_separation*(1 if z_offset<0 else -1), atoms, bonds, angles, dihedrals)
pushed_atoms.append( atoms[-15] )
else:
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
if xi==0 or yi==0:
held_atoms.append( atoms[-15] )
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
else:
for xi in range(box_size[0]/S):
x = xi*S - box_size[0]/2
for yi in range(box_size[1]/S):
y = yi*S - box_size[1]/2
if (xi%2)==(yi%2):
if xi==3 and yi==3:
tail.add_to(x, y, z+z_separation*(1 if z_offset<0 else -1), atoms, bonds, angles, dihedrals)
else:
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
else:
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
for a in atoms[::-1]:
if a.element=='N':
if xi==3 and yi==3:
pushed_atoms.append( a )
elif xi==0 or yi==0:
held_atoms.append( a )
break
#filetypes.write_xyz('', atoms, xyz_file)
print pushed_atoms[0].z
return
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
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]
for xi in range(box_size[0]/solvent_spacing[0]):
for yi in range(box_size[1]/solvent_spacing[1]):
for zi in range(box_size[2]/solvent_spacing[2]):
x, y, z = xi*solvent_spacing[0]-box_size[0]/2, yi*solvent_spacing[1]-box_size[1]/2, zi*solvent_spacing[2]-box_size[2]/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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.45
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 = True
directory = 'lammps'
os.chdir(directory)
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')
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')
f.write('''
dump 1 all xyz '''+str(int(10000*timescale))+''' '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed epair press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
group held_atoms id '''+(' '.join([str(a.index) for a in held_atoms]))+'''
group pushed_atoms id '''+(' '.join([str(a.index) for a in pushed_atoms]))+'''
fix no_z held_atoms planeforce 0.0 0.0 1.0
fix hold pushed_atoms smd cvel 100.0 0.0 tether NULL NULL 100.0 0.0
fix no_z_temp pushed_atoms planeforce 0.0 0.0 1.0 #since smd is not enforced during minimization
minimize 0.0 1.0e-8 1000 100000
unfix no_z_temp
timestep 2.0
fix relax all npt temp 10.0 10.0 50 aniso '''+str(P)+' '+str(P)+''' 500
run 1000
unfix relax
velocity all create '''+str(T)+''' 1 rot yes dist gaussian
velocity held_atoms set 0.0 0.0 0.0
fix press all npt temp '''+str(T)+' '+str(T)+''' 100 aniso '''+str(P)+' '+str(P)+''' 1000
fix average all ave/time 1 1000 1000 c_thermo_pe f_hold[4] f_hold[6]
thermo 1000
thermo_style custom f_average[1] f_average[2] f_average[3]
run '''+str(int(50000*timescale))+'''
write_restart '''+run_name+'.restart\n')
f.close()
if True: #start multiple processes
#os.system('nohup ~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
#print 'Running', 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) )
else:
os.system('~/lammps2/src/lmp_g++ -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
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 react_dots(
params,
dot_size1,
dot_size2,
prior_run_name1,
prior_run_name2,
random_seed=1,
run_name_prefix="react_",
on_queue=True,
method="metadynamics",
):
random_s = str(random_seed)
random.seed(random_seed)
run_name = run_name_prefix + str(dot_size1) + "_" + str(dot_size2)
spoc = utils.Molecule("/fs/home/jms875/Documents/nanocrystals/pb_oleate_hydrate_morse/" + spoc_name + ".arc")
atoms1, bonds1, angles1, dihedrals1 = cPickle.load(open("lammps/" + prior_run_name1 + ".pickle", "rb"))
atoms1, bonds1, angles1, dihedrals1 = remove_unattached_ligands(atoms1, bonds1, angles1, dihedrals1, spoc)
atoms2, bonds2, angles2, dihedrals2 = cPickle.load(open("lammps/" + prior_run_name2 + ".pickle", "rb"))
atoms2, bonds2, angles2, dihedrals2 = remove_unattached_ligands(atoms2, bonds2, angles2, dihedrals2, spoc)
atoms1_xyz = filetypes.parse_xyz(prior_run_name1 + ".xyz")
atoms2_xyz = filetypes.parse_xyz(prior_run_name2 + ".xyz")
goal_atoms = filetypes.parse_xyz("dot" + str(dot_size1 + dot_size2) + ".xyz")
# set starting coordinates
for a, b in zip(atoms1, atoms1_xyz):
a.x = b.x
a.y = b.y
a.z = b.z
for a, b in zip(atoms2, atoms2_xyz):
a.x = b.x
a.y = b.y
a.z = b.z
atoms = atoms1 + atoms2
bonds = bonds1 + bonds2
angles = angles1 + angles2
dihedrals = dihedrals1 + dihedrals2
# make sure atom types are the same in atom1 and atom2
atom_types_by_type_index = dict([(t.type.index, t.type) for t in atoms])
for i, a in enumerate(atoms):
a.type = atom_types_by_type_index[a.type.index]
a.index = i + 1
if coul_on and a.type.index in params:
a.charge = params[a.type.index]
else:
a.charge = a.type.charge
atom_types = dict([(t.type, True) for t in atoms]).keys()
atom_types.sort(key=lambda t: -t.element - t.index * 0.00001)
offset = (
radius_of_gyration([a for a in atoms1 if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
+ radius_of_gyration([a for a in atoms2 if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
+ 10.0
)
offset_vector = utils.matvec(utils.rand_rotation(), [offset, offset, offset])
rot = utils.rand_rotation()
for a in atoms2: # offset by random orientation vector
a.x, a.y, a.z = utils.matvec(rot, [a.x, a.y, a.z])
a.x += offset_vector[0]
a.y += offset_vector[1]
a.z += offset_vector[2]
box_size = [
15.0 + max([a.x for a in atoms]) - min([a.x for a in atoms]),
15.0 + max([a.y for a in atoms]) - min([a.y for a in atoms]),
15.0 + max([a.z for a in atoms]) - min([a.z for a in atoms]),
]
# goal_atoms = cPickle.load( open('lammps/dot'+str(dot_size1+dot_size2)+'.pickle', 'rb') )[0]
# filetypes.write_xyz('out_meta', atoms)
# exit()
os.chdir("lammps")
save_to_file(atoms, bonds, angles, dihedrals, atom_types, run_name)
lammps.write_data_file_general(
atoms, bonds, angles, dihedrals, box_size, run_name, atom_types=atom_types, pair_coeffs_included=False
)
os.system("cp ../" + sys.argv[0] + " " + run_name + ".py")
starting_rxn_coord = radius_of_gyration(
[a for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")]
)
print len([a for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
goal_rxn_coord = radius_of_gyration(goal_atoms[0 : 2 * (dot_size1 + dot_size2)])
colvars_file = open(run_name + ".colvars", "w")
colvars_file.write(
"""
colvarsTrajFrequency 10000
colvarsRestartFrequency 100000
colvar {
name gyr
width 0.1 #size of bins, in Angstroms
upperBoundary """
+ str(starting_rxn_coord)
+ """ #two separate dots
lowerBoundary """
+ str(goal_rxn_coord)
+ """ #one unified dot
lowerwallconstant 10.0
upperwallconstant 10.0
gyration {
atoms {
atomNumbers """
+ (" ".join([str(a.index) for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")]))
+ """
}
}
}
"""
)
if method.lower() == "abf":
colvars_file.write(
"""
abf {
colvars gyr
hideJacobian # when using distance-based colvar: makes pmf flat at infinity
fullSamples 1000
}
"""
)
elif method.lower() == "metadynamics":
colvars_file.write(
"""
metadynamics {
colvars gyr
hillWeight 0.1
newHillFrequency 1000
}
"""
)
else:
raise Exception('Invalid free energy method "%s"' % method)
colvars_file.close()
f = open(run_name + ".in", "w")
write_input_header(f, run_name, atom_types, read_restart=False)
f.write(
"""
dump 1 all xyz 10000 """
+ run_name
+ """.xyz
minimize 0.0 1.0e-8 10000 1000
neigh_modify check yes every 1 delay 0
thermo_style custom pe temp
thermo 10000
restart 100000 """
+ run_name
+ """.restart1 """
+ run_name
+ """.restart2
fix motion all nve
fix implicit_solvent all langevin 400.0 400.0 100.0 """
+ random_s
+ """ zero yes gjf yes
fix col all colvars """
+ run_name
+ """.colvars output """
+ run_name
+ """ seed """
+ random_s
+ """ tstat implicit_solvent
velocity all create 400.0 """
+ random_s
+ """ mom yes
timestep 2.0
thermo_style custom step temp etotal pe ke epair ebond f_col tpcpu
run """
+ str(int(1e7))
+ """
write_restart """
+ run_name
+ """.restart
"""
)
f.close()
# run_job(run_name, on_queue)
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(run_name):
utils.Molecule.set_params('oplsaa4.prm')
tail = utils.Molecule('acrylonitrile2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x-2.0
atoms = []
bonds = []
angles = []
dihedrals = []
added_atoms = []
S = 2.4
R = 8.0
for phi_i in range(math.pi*R/S):
phi = S/R*0.5 + S/R*phi_i
z = R*math.cos(phi)
r = (R**2 - z**2)**0.5
N_theta = int(math.pi*2*r/S)
for theta_i in range(N_theta):
theta = S/r + (math.pi*2)*theta_i/N_theta
x, y = R*math.cos(theta)*math.sin(phi), R*math.sin(theta)*math.sin(phi)
weighted_charge = 0.0
for added in added_atoms:
weight = 1/( (x-added.x)**2 + (y-added.y)**2 + (z-added.z)**2 )
weighted_charge += weight*added.charge
charge = 1 if weighted_charge<0 else -1
added_atoms.append( utils.Struct( x=x, y=y, z=z, theta=theta, phi=phi, charge=charge ) )
for added in added_atoms:
x, y, z, theta, phi = added.x, added.y, added.z, added.theta, added.phi
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
if added.charge>0:
for a in tail.atoms:
a.x, a.y, a.z = -a.z-7, a.y, -a.x
c1,c2,s1,s2 = math.cos(theta),math.cos(phi+math.pi/2),math.sin(theta),math.sin(phi+math.pi/2)
m = [ [c1*c2, -s1, c1*s2], [c2*s1, c1, s1*s2], [-s2, 0., c2] ]
tail.rotate(m)
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
else:
for a in tail.atoms:
a.x, a.y, a.z = -a.z-7, a.y, -a.x
c1,c2,s1,s2 = math.cos(theta),math.cos(phi+math.pi/2),math.sin(theta),math.sin(phi+math.pi/2)
m = [ [c1*c2, -s1, c1*s2], [c2*s1, c1, s1*s2], [-s2, 0., c2] ]
tail.rotate(m)
x*=0.7; y*-0.7; z*=0.7
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
box_size = [R*2+30]*3
T = 94.0
P = 1.45
filetypes.write_xyz('out', atoms)
sys.exit()
directory = 'lammps'
os.chdir(directory)
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 = True
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')
if is_charged:
# f.write('pair_style lj/cut/coul/long 8.0\n')
f.write('pair_style lj/cut/coul/cut 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')
f.write('''thermo 0
dump 1 all xyz 100 '''+run_name+'''.xyz
thermo_modify line multi format float %14.6f
thermo 1000
minimize 0.0 1.0e-8 1000 100000
velocity all create '''+str(T)+''' 1 rot yes dist gaussian
fix dynamics all nve
fix solvent all langevin '''+str(T)+' '+str(5*T)+''' 100 1337
timestep 2.0
neigh_modify check yes every 1 delay 0
run 100
''')
f.close()
if False: #start multiple processes
os.system('nohup ~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log &> /dev/null &' % (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 make_lattice(params, system_size, prior_run_name, lc_x=1, lc_y=1, lc_z=1, random_seed=1, run_name_prefix='lattice_', on_queue=True):
atoms, bonds, angles, dihedrals = [], [], [], []
x, y, z = 0, 0, 0
spacer = utils.Molecule('ma.arc')
for xi in range(system_size):
x, y, z = 0, 0, 0
for yi in range(system_size):
x, y, z = 0, 0, 0
for zi in range(system_size):
x=xi*lc_x
y=yi*lc_y
z=zi*lc_z
unbonded_atoms = filetypes.parse_xyz('/fs/home/jar528/Desktop/nano/xyz/unbonded.xyz')
for a in unbonded_atoms:
a.x += x
a.y += y
a.z += z
atoms = atoms + unbonded_atoms
spacer.add_to(x, y, z, atoms, bonds, angles, dihedrals)
iodine_type = [t for t in utils.Molecule.atom_types if t.element_name=='I'][-1]
lead_type = [t for t in utils.Molecule.atom_types if t.element_name=='Pb'][-1]
for a in atoms:
if a.element=='I':
a.type=iodine_type
if a.element=='Pb':
a.type=lead_type
#filetypes.write_xyz('/fs/home/jar528/Desktop/nano/out', atoms)
#exit()
random_s = str(random_seed)
random.seed(random_seed)
run_name = run_name_prefix+str(system_size)
# make sure atom types are the same in atom1 and atom2
atom_types_by_type_index = dict( [(t.type.index,t.type) for t in atoms] )
for i,a in enumerate(atoms):
a.type = atom_types_by_type_index[ a.type.index ]
a.index = i+1
if coul_on and a.type.index in params:
a.charge = params[a.type.index]
else:
a.charge = a.type.charge
atom_types = dict( [(t.type,True) for t in atoms] ).keys()
atom_types.sort(key=lambda t:-t.element-t.index*0.00001)
box_size = [ 3.24+max([a.x for a in atoms])-min([a.x for a in atoms]),
3.24+max([a.y for a in atoms])-min([a.y for a in atoms]),
3.24+max([a.z for a in atoms])-min([a.z for a in atoms]) ]
os.chdir('lammps')
save_to_file( atoms, bonds, angles, dihedrals, atom_types, run_name )
lammps.write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name, atom_types=atom_types, pair_coeffs_included=False)
os.system('cp ../'+sys.argv[0]+' '+run_name+'.py')
f = open(run_name+'.in', 'w')
write_input_header(f, run_name, atom_types, read_restart=False)
f.write('''
dump 1 all xyz 10000 '''+run_name+'''.xyz
minimize 0.0 1.0e-8 10000 1000
neigh_modify check yes every 1 delay 0
thermo 10000
restart 100000 '''+run_name+'''.restart1 '''+run_name+'''.restart2
#fix motion all nve
#fix implicit_solvent all langevin 400.0 400.0 1000.0 '''+random_s+''' zero yes gjf yes
fix motion all npt temp 450.0 450.0 100.0 aniso 1.0 1.0 1000.0
velocity all create 400.0 '''+random_s+''' mom yes
timestep 2.0
thermo_style custom step temp etotal pe tpcpu
run '''+str(int(1e6))+'''
#thermo 1
#run 1000
minimize 0.0 1.0e-8 10000 1000
write_restart '''+run_name+'''.restart
''')
f.close()
run_job(run_name, on_queue)
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 run():
utils.Molecule.set_params('oplsaa4.prm')
solvent = utils.Molecule('methane.arc')
if False:
tail = utils.Molecule('propanenitrile.arc')
z_off_1 = 3.0
z_off_2 = -5.5
else:
tail = utils.Molecule('hexanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_off_1 = 0.0
z_off_2 = 6.5
directory = 'lammps'
os.chdir(directory)
n_steps = 1
for step in range(0,n_steps):
atoms = []
bonds = []
angles = []
dihedrals = []
S = 3.5
box_size = [21.,21.,35.]
theta = 0; z = 0.0
molecules_not_added = 0
held_Ns = []
pushed_Ns = []
for xi in range(box_size[0]/S):
x = xi*S - box_size[0]/2
for yi in range(box_size[1]/S):
y = yi*S - box_size[1]/2
if (xi%2)==(yi%2):
tail.add_to(x, y, z+z_off_1, atoms, bonds, angles, dihedrals)
else:
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_off_2
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
if (xi,yi) in [(3,3)]:
for a in atoms[::-1]:
if a.element=='N':
pushed_Ns.append(a)
break
elif (xi,yi) in [(0,0)]:
for a in atoms[::-1]:
if a.element=='N':
held_Ns.append(a)
break
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
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]
for xi in range(box_size[0]/solvent_spacing[0]):
for yi in range(box_size[1]/solvent_spacing[1]):
for zi in range(box_size[2]/solvent_spacing[2]):
x, y, z = xi*solvent_spacing[0]-box_size[0]/2, yi*solvent_spacing[1]-box_size[1]/2, zi*solvent_spacing[2]-box_size[2]/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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
T_hot = T*4.2
P = 1.45
#filetypes.write_xyz('out', atoms)
#sys.exit(0)
run_name = 'azoto_hot__0'
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 = True
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')
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')
f.write('''thermo 0
dump 1 all xyz 1000 '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed epair press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
timestep 4.0
neigh_modify check yes every 1 delay 0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
thermo 1000
fix relax all npt temp 10.0 10.0 50 aniso '''+str(P)+' '+str(P)+''' 500
run 1000
unfix relax
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
run 1000
group held_Ns id '''+(' '.join([str(N.index) for N in held_Ns]))+'''
group pushed_Ns id '''+(' '.join([str(N.index) for N in pushed_Ns]))+'''
#fix push1 held_Ns smd cvel 20.0 -0.00001 tether NULL NULL 100.0 0.0
#fix push2 pushed_Ns smd cvel 20.0 0.00001 tether NULL NULL 100.0 0.0
unfix press
group membrane id <= '''+str(atom_count)+'''
group solvent subtract all membrane
fix press1 membrane npt temp '''+str(T_hot)+' '+str(T_hot)+''' 100 aniso '''+str(P)+' '+str(P)+''' 1000
fix press2 solvent nvt temp '''+str(T_hot)+' '+str(T_hot)+''' 100
#thermo_style custom epair f_push1[7] f_push2[7]
thermo 100
run 10000
''')
f.close()
if False: #start multiple processes
os.system('nohup ~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
print 'Running', run_name
else:
os.system('~/lammps2/src/lmp_g++ -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
def run(mode, timescale):
run_name = 'bend11_'+str(mode)
if mode==3:
tail = utils.Molecule('propanenitrile.arc')
z_offset = -4.5
elif mode==4:
tail = utils.Molecule('butanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.5
elif mode==5:
tail = utils.Molecule('pentanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==6:
tail = utils.Molecule('hexanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==7:
tail = utils.Molecule('aminopropane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 2.5
elif mode==8:
tail = utils.Molecule('aminobutane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, -a.x
z_offset = 3.5
elif mode==9:
tail = utils.Molecule('aminopentane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==10:
tail = utils.Molecule('aminohexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==11:
tail = utils.Molecule('hexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 8.0
elif mode==12:
tail = utils.Molecule('hcn2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -3.5
elif mode==13:
tail = utils.Molecule('cyanoacetylene2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 0.0
elif mode==14:
tail = utils.Molecule('acrylonitrile2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
elif mode==15:
tail = utils.Molecule('cyanoallene2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.0
elif mode==16:
tail = utils.Molecule('acetonitrile2.arc')
z_offset = 0.0
elif mode==17:
tail = utils.Molecule('hc5n2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
directory = 'lammps'
os.chdir(directory)
atoms = []
bonds = []
angles = []
dihedrals = []
S_count = 12
S = 3.5
box_size = [ S_count*S ]*3
theta = 0; z = 0.0
molecules_not_added = 0
pushable = []
if mode==11:
for xi in range(S_count):
x = xi*S - box_size[0]/2
for yi in range(S_count):
y = yi*S - box_size[1]/2
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
push_r = S * ( (xi-S_count/2)**2 + (yi-S_count/2)**2 )**0.5
if xi==0 or yi==0:
push_r = 100.0
atoms[-15].push_r = push_r
pushable.append( atoms[-15] )
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
atoms[-15].push_r = push_r
pushable.append( atoms[-15] )
else:
for xi in range(S_count):
x = xi*S - box_size[0]/2
for yi in range(S_count):
y = yi*S - box_size[1]/2
if (xi%2)==(yi%2):
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
else:
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
for a in atoms[::-1]:
if a.element=='N':
a.push_r = 100.0 if (xi==0 or yi==0) else S * ( (xi-S_count/2)**2 + (yi-S_count/2)**2 )**0.5
pushable.append(a)
break
#for a in pushable:
# a.element = str(int(a.push_r))
#for a in atoms:
# print a.element
#filetypes.write_xyz('out', atoms)
#sys.exit(0)
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
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]
for xi in range(int(box_size[0]/solvent_spacing[0])):
for yi in range(int(box_size[1]/solvent_spacing[1])):
for zi in range(int(box_size[2]/solvent_spacing[2])):
x, y, z = xi*solvent_spacing[0]-box_size[0]/2, yi*solvent_spacing[1]-box_size[1]/2, zi*solvent_spacing[2]-box_size[2]/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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.45
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 = True
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')
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')
f.write('''thermo 0
dump 1 all xyz '''+str(int(10000*timescale))+''' '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed epair press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
timestep 4.0
neigh_modify check yes every 1 delay 0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
thermo 1000
fix relax all npt temp 10.0 10.0 50 aniso '''+str(P)+' '+str(P)+''' 500
run 1000
unfix relax
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
run '''+str(int(25000*timescale))+'''
''')
push_groups = [[a for a in pushable if a.push_r<=R and a.push_r>(R-0.01)] for R in [0.01*ri for ri in range(0,1000)]]
push_groups = [p for p in push_groups if p]
for p_i,p in enumerate(push_groups):
f.write('group push_g'+str(p_i)+' id '+(' '.join([str(a.index) for a in p]))+'\n')
r = p[0].push_r
max_r = 10.0
v = 0.5 * 1e-6*( max_r**2 - r**2 )**0.5 / timescale
print r, v, 250000*timescale*4*v
f.write('fix push_%d push_g%d smd cvel 20.0 %e tether NULL NULL 100.0 0.0\n' % (p_i, p_i, v) )
f.write('group held_atoms id '+(' '.join([str(a.index) for a in pushable if a.push_r==100.0]))+'\nfix zrest held_atoms spring/self 20.0 z\n')
f.write('thermo_style custom ' + ( ' '.join(['f_push_%d[6] f_push_%d[7]' % (p_i,p_i) for p_i,p in enumerate(push_groups)]) ) + '\n')
f.write('''
thermo '''+str(int(1000*timescale))+'''
run '''+str(int(250000*timescale))+'''
''')
f.close()
if True: #start multiple processes
os.system('nohup ~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
print 'Running', run_name
else:
os.system('~/lammps2/src/lmp_g++ -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
def run(solvent_ratio):
utils.Molecule.set_params('oplsaa4.prm')
tail = utils.Molecule('hexanenitrile.arc')
solvent = utils.Molecule('methane.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
directory = 'lammps'
os.chdir(directory)
n_steps = 1
for step in range(0,n_steps):
atoms = []
bonds = []
angles = []
dihedrals = []
S = 3.5
box_size = [20,20,20]
theta = 0; z = 0.0
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
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]
for x in utils.frange(-box_size[0]/2, box_size[0]/2-solvent_spacing[0], solvent_spacing[0]):
for y in utils.frange(-box_size[1]/2, box_size[1]/2-solvent_spacing[1], solvent_spacing[1]):
for z in utils.frange(-box_size[2]/2, box_size[2]/2-solvent_spacing[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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.45
print (len(atoms)-atom_count)/len(solvent.atoms)
filetypes.write_xyz('out', atoms)
run_name = 'azoto_solv__'+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 = True
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')
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')
f.write('''thermo 0
dump 1 all xyz 10000 '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed evdwl ecoul elong press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
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)+''' 500
timestep 4.0
neigh_modify check yes every 1 delay 0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
thermo 100
run 25000
unfix press
fix dynamics all nvt temp '''+str(T)+' '+str(T)+''' 100
thermo_style custom epair pe etotal
thermo 1
run 25000
''')
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) )
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(R):
atoms = []
bonds = []
angles = []
dihedrals = []
added_atoms = []
S = 3.5
for phi_i in range(math.pi*R/S):
phi = S/R*0.5 + S/R*phi_i
z = R*math.cos(phi)
r = (R**2 - z**2)**0.5
N_theta = int(math.pi*2*r/S)
for theta_i in range(N_theta):
theta = S/r + (math.pi*2)*theta_i/N_theta
x, y = R*math.cos(theta)*math.sin(phi), R*math.sin(theta)*math.sin(phi)
weighted_charge = 0.0
for added in added_atoms:
weight = 1/( (x-added.x)**2 + (y-added.y)**2 + (z-added.z)**2 )
weighted_charge += weight*added.charge
charge = 1 if weighted_charge<0 else -1
added_atoms.append( utils.Struct( x=x, y=y, z=z, theta=theta, phi=phi, charge=charge ) )
added_atoms.append( utils.Struct( x=0., y=0., z=0., theta=0., phi=0., charge=1 ) )
for added in added_atoms:
x, y, z, theta, phi = added.x, added.y, added.z, added.theta, added.phi
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
if added.charge>0:
for a in tail.atoms:
a.x, a.y, a.z = -a.z-7, a.y, -a.x
c1,c2,s1,s2 = math.cos(theta),math.cos(phi+math.pi/2),math.sin(theta),math.sin(phi+math.pi/2)
m = [ [c1*c2, -s1, c1*s2], [c2*s1, c1, s1*s2], [-s2, 0., c2] ]
tail.rotate(m)
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
else:
for a in tail.atoms:
a.x, a.y, a.z = a.z, a.y, a.x
c1,c2,s1,s2 = math.cos(theta),math.cos(phi+math.pi/2),math.sin(theta),math.sin(phi+math.pi/2)
m = [ [c1*c2, -s1, c1*s2], [c2*s1, c1, s1*s2], [-s2, 0., c2] ]
tail.rotate(m)
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
atom_count = len(atoms)
box_size = [R*2+20]*3
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+0.0 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]
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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.5
directory = 'lammps'
if not os.path.isdir(directory):
os.mkdir(directory)
os.chdir(directory)
run_name = 'azo_hex_r'+str(R)
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
neigh_modify exclude molecule all
group test_molecules id <= '''+str(atom_count)+'''
compute 1 all pair/local eng
compute 2 test_molecules reduce sum c_1
minimize 0.0 1.0e-8 1000 100000
velocity all create '''+str(T)+''' 1 rot yes dist gaussian
fix dynamics all nvt temp '''+str(T)+' '+str(T)+''' 100
timestep 4.0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
run 2500
thermo_style custom c_2
thermo 1
run 1000
''')
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) )
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(mode, timescale):
run_name = 'smd20_'+str(mode)
utils.Molecule.set_params('oplsaa4.prm')
solvent = utils.Molecule('methane.arc')
#solvent = utils.Molecule('benzene2.arc')
#solvent = utils.Molecule('hexane2.arc')
box_size = [21.,21.,42.]
S = 3.5
if mode==3:
tail = utils.Molecule('propanenitrile.arc')
z_offset = -4.5
elif mode==4:
tail = utils.Molecule('butanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.5
elif mode==5:
tail = utils.Molecule('pentanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==6:
tail = utils.Molecule('hexanenitrile.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==7:
tail = utils.Molecule('aminopropane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 2.5
elif mode==8:
tail = utils.Molecule('aminobutane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, -a.x
z_offset = 3.5
elif mode==9:
tail = utils.Molecule('aminopentane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 5.0
elif mode==10:
tail = utils.Molecule('aminohexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 6.5
elif mode==11:
tail = utils.Molecule('hexane2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 8.0
elif mode==12:
tail = utils.Molecule('hcn2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
S = 3.0
z_offset = -0.5
elif mode==13:
tail = utils.Molecule('cyanoacetylene2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -2.0
elif mode==14:
tail = utils.Molecule('acrylonitrile2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
elif mode==15:
tail = utils.Molecule('cyanoallene2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = 4.0
elif mode==16:
tail = utils.Molecule('acetonitrile2.arc')
z_offset = 2.0
elif mode==17:
tail = utils.Molecule('hc5n2.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
z_offset = -4.0
directory = 'lammps'
os.chdir(directory)
atoms = []
bonds = []
angles = []
dihedrals = []
theta = 0; z = 0.0
molecules_not_added = 0
held_atoms = []
pushed_atoms = []
if mode==11:
for xi in range(box_size[0]/S):
x = xi*S - box_size[0]/2
for yi in range(box_size[1]/S):
y = yi*S - box_size[1]/2
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
if xi==3 and yi==3:
pushed_atoms.append( atoms[-15] )
elif xi==0 or yi==0:
held_atoms.append( atoms[-15] )
else:
for xi in range(box_size[0]/S):
x = xi*S - box_size[0]/2
for yi in range(box_size[1]/S):
y = yi*S - box_size[1]/2
if (xi%2)==(yi%2):
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
else:
old_atom_positions = [(a.x, a.y, a.z) for a in tail.atoms]
for a in tail.atoms:
a.z = -a.z+z_offset
a.y = -a.y
tail.add_to(x, y, z, atoms, bonds, angles, dihedrals)
for i,a in enumerate(tail.atoms): a.x, a.y, a.z = old_atom_positions[i]
for a in atoms[::-1]:
if a.element=='N':
if xi==3 and yi==3:
pushed_atoms.append( a )
elif xi==0 or yi==0:
held_atoms.append( a )
break
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
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]
for xi in range(box_size[0]/solvent_spacing[0]):
for yi in range(box_size[1]/solvent_spacing[1]):
for zi in range(box_size[2]/solvent_spacing[2]):
x, y, z = xi*solvent_spacing[0]-box_size[0]/2, yi*solvent_spacing[1]-box_size[1]/2, zi*solvent_spacing[2]-box_size[2]/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 Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.45
#filetypes.write_xyz(run_name, atoms)
#os.chdir('..')
#return
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 = True
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')
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')
f.write('''
dump 1 all xyz '''+str(int(10000*timescale))+''' '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed epair press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
timestep 4.0
neigh_modify check yes every 1 delay 0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
fix relax all npt temp 10.0 10.0 50 aniso '''+str(P)+' '+str(P)+''' 500
run 1000
unfix relax
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
thermo '''+str(int(100*timescale))+'''
run '''+str(int(25000*timescale))+'''
group held_atoms id '''+(' '.join([str(a.index) for a in held_atoms]))+'''
group pushed_atoms id '''+(' '.join([str(a.index) for a in pushed_atoms]))+'''
fix zrest held_atoms spring/self 100.0 z
fix push pushed_atoms smd cvel 100.0 '''+str((-1 if z_offset<0 else 1)*0.00001/timescale)+''' tether NULL NULL 100.0 0.0
thermo_style custom f_push[6] f_push[7] f_zrest
run '''+str(int(250000*timescale))+'''
''')
f.close()
if True: #start multiple processes
os.system('nohup ~/lammps2/src/lmp_g++ -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
print 'Running', run_name
else:
os.system('~/lammps2/src/lmp_g++ -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
def run(test_molecule_filename, makefile):
utils.Molecule.set_params('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:]=='e2': 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]
solvent_spacing[2] += 1.0
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('..')