def unweighted_COM(start_atoms,end_atoms):
start_comx = sum(a.x for a in start_atoms)/len(start_atoms)
start_comy = sum(a.y for a in start_atoms)/len(start_atoms)
start_comz = sum(a.z for a in start_atoms)/len(start_atoms)
end_comx = sum(a.x for a in end_atoms)/len(end_atoms)
end_comy = sum(a.y for a in end_atoms)/len(end_atoms)
end_comz = sum(a.z for a in end_atoms)/len(end_atoms)
startx = [a.x-start_comx for a in start_atoms]
starty = [a.y-start_comy for a in start_atoms]
startz = [a.z-start_comz for a in start_atoms]
endx = [a.x-end_comx for a in end_atoms]
endy = [a.y-end_comy for a in end_atoms]
endz = [a.z-end_comz for a in end_atoms]
for i in range(len(start_atoms)):
start_atoms[i].x = startx[i]
start_atoms[i].y = starty[i]
start_atoms[i].z = startz[i]
start_com = np.array([[start_comx],[start_comy],[start_comz]])
end_com = np.array([[end_comx,end_comy,end_comz]])
filetypes.write_xyz('out',start_atoms)
return startx,starty,startz,endx,endy,endz,start_com,end_com
def acetone_and_pbi2():
acetone1 = gaussian.atoms('acetone')
pbi2 = filetypes.parse_xyz('xyz/Optimized Molecules/pbi2.xyz')
for atom in acetone1:
atom.x = atom.x + 10
atoms = acetone1+pbi2
filetypes.write_xyz('pbi2_1acetone', atoms)
def weighted_COM(start_atoms,end_atoms):
MASS_BY_TYPE = {'Pb': 207.2, 'S': 32.065, 'O': 15.9994, 'H': 1.0079, 'C': 12.0107}
# shift all structures so that origin is the COM:
start_comx = 0.0
start_comy = 0.0
start_comz = 0.0
start_mtot = 0.0
end_comx = 0.0
end_comy = 0.0
end_comz = 0.0
end_mtot = 0.0
# calculate center of mass
for s,e in zip(start_atoms, end_atoms):
start_comx += s.x*MASS_BY_TYPE[ s.element ]
start_comy += s.y*MASS_BY_TYPE[ s.element ]
start_comz += s.z*MASS_BY_TYPE[ s.element ]
start_mtot += MASS_BY_TYPE[ s.element ]
end_comx += e.x*MASS_BY_TYPE[ e.element ]
end_comy += e.y*MASS_BY_TYPE[ e.element ]
end_comz += e.z*MASS_BY_TYPE[ e.element ]
end_mtot += MASS_BY_TYPE[ e.element ]
start_comx = start_comx/start_mtot
start_comy = start_comy/start_mtot
start_comz = start_comz/start_mtot
end_comx = end_comx/end_mtot
end_comy = end_comy/end_mtot
end_comz = end_comz/end_mtot
startx = [a.x-start_comx for a in start_atoms]
starty = [a.y-start_comy for a in start_atoms]
startz = [a.z-start_comz for a in start_atoms]
endx = [a.x-end_comx for a in end_atoms]
endy = [a.y-end_comy for a in end_atoms]
endz = [a.z-end_comz for a in end_atoms]
for i in range(len(start_atoms)):
start_atoms[i].x = startx[i]
start_atoms[i].y = starty[i]
start_atoms[i].z = startz[i]
start_com = np.array([[start_comx],[start_comy],[start_comz]])
end_com = np.array([[end_comx,end_comy,end_comz]])
filetypes.write_xyz('out',start_atoms)
return startx,starty,startz,endx,endy,endz,start_com,end_com
import math, copy, sys, random, re, os, cPickle, shutil
sys.path.append("/fs/home/jms875/Library")
import gaussian, filetypes, utils
name = sys.argv[1]
if len(sys.argv) == 3:
low = 0
count = int(sys.argv[2])
if len(sys.argv) == 4:
low = int(sys.argv[2])
count = int(sys.argv[3])
f = open('out.xyz', 'w')
energies = []
for step in range(low, count):
energy, atoms = gaussian.parse_atoms(name % step, check_convergence=False)
filetypes.write_xyz('', atoms, f)
print energy, int(gaussian.parse_atoms(name % step) != None)
energies.append(energy)
def matplot(y):
import matplotlib.pyplot as plt
plt.plot(y, marker='.')
plt.show()
f.close()
energies = [(e - energies[0]) * 627.5 for e in energies]
matplot(energies)
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 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(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(filename):
tail = utils.Molecule(filename+'.arc')
atoms = []
bonds = []
angles = []
dihedrals = []
tail.add_to(0., 0., 0., atoms, bonds, angles, dihedrals)
tail.add_to(0., 5., 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 = 'bind3_'+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 2500 '''+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
group aa id <= '''+str(len(atoms)/2)+'''
group bb subtract all aa
compute 1 aa group/group bb kspace yes
thermo_style custom c_1
run 0
''')
f.close()
os.system('lammps -in '+run_name+'.in -log '+run_name+'.log')
os.chdir('..')
for i,line in enumerate(open(directory+'/'+run_name+'.xyz').readlines()[ -len(atoms) : ]):
columns = line.split()
index, x, y, z = columns
atoms[i].x, atoms[i].y, atoms[i].z = float(x), float(y), float(z)
filetypes.write_xyz(run_name, atoms)