def binding2():
for n in [
'propanenitrile', 'butanenitrile', 'pentanenitrile',
'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2',
'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2',
'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2'
]:
'''
try:
contents = open('lammps/bind3_'+n+'.log').read()
opls_binding_e = float(re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
pair = gaussian.parse_atoms('gaussian/'+n+'_opt.log')[0]
lone1 = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
lone2 = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
print n, opls_binding_e, 627.5*(pair - lone1 - lone2)
except: print n
'''
#(Optimized pair energy) - 2*(optimized single energy) - (BSSE of optimized pair)
try:
contents = open('lammps/bind3_' + n + '.log').read()
opls_pair = float(re.findall('TotEng\s+=\s+(\S+)', contents)[-1])
opls_single = float(re.findall('TotEng\s+=\s+(\S+)', contents)[-1])
pair = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt1.log')[0]
single = gaussian.parse_atoms('gaussian/' + n + '_0.log')[0]
print n, opls_binding_e, 627.5 * (pair - lone1 - lone2)
except:
print n
def binding2():
for n in ['propanenitrile', 'butanenitrile', 'pentanenitrile', 'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2', 'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2', 'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2']:
'''
try:
contents = open('lammps/bind3_'+n+'.log').read()
opls_binding_e = float(re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
pair = gaussian.parse_atoms('gaussian/'+n+'_opt.log')[0]
lone1 = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
lone2 = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
print n, opls_binding_e, 627.5*(pair - lone1 - lone2)
except: print n
'''
#(Optimized pair energy) - 2*(optimized single energy) - (BSSE of optimized pair)
try:
contents = open('lammps/bind3_'+n+'.log').read()
opls_pair = float(re.findall('TotEng\s+=\s+(\S+)', contents)[-1])
opls_single = float(re.findall('TotEng\s+=\s+(\S+)', contents)[-1])
pair = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.log')[0]
single = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
print n, opls_binding_e, 627.5*(pair - lone1 - lone2)
except: print n
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 analyze_binding():
for n in ['propanenitrile', 'butanenitrile', 'pentanenitrile', 'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2', 'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2', 'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2']:
contents = open('lammps/bind3_'+n+'.log').read()
opls_binding_e = float(re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
try:
e_pair = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.1.log', check_convergence=False)[0]
except:
e_pair = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.log', check_convergence=False)[0]
try:
e_pair_scrf = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.1.log', check_convergence=False)[0]
except:
e_pair_scrf = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.log', check_convergence=False)[0]
e_single = gaussian.parse_atoms('gaussian/'+n+'_0.log')[0]
e_single_scrf = gaussian.parse_atoms('gaussian/'+n+'_1.log')[0]
try:
bsse = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a.log')[0] + gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b.log')[0] - gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a_Bq.log')[0] - gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b_Bq.log')[0]
except:
print 1, n
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a_Bq.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b_Bq.log') is None
bsse = 0.0
try:
bsse_scrf = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a.log')[0] + gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b.log')[0] - gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a_Bq.log')[0] - gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b_Bq.log')[0]
except:
print 2, n
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a_Bq.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b_Bq.log') is None
bsse_scrf = 0.0
#No such file or directory: 'gaussian/bind3_aminopentane2_opt2b_Bq.log
#No such file or directory: 'gaussian/bind3_aminobutane2_opt2a_Bq.log'
#print n, opls_binding_e, e_pair, e_single, bsse, e_pair_scrf, e_single_scrf, bsse_scrf
print n, ',', opls_binding_e, ',', (e_pair-2*e_single+bsse)*627, ',', (e_pair_scrf-2*e_single_scrf+bsse_scrf)*627
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
gaussian.job(atoms, 'HSEH1PBE/cc-pVDZ', 'batch', name, route, previous=previous_job)
return name
def binding_energy_dz(job_total, job_A, job_B, zero_indexed_atom_indices_A):
AB = gaussian.atoms(job_total)
AB_A = copy.deepcopy(AB)
for i,atom in enumerate(AB_A):
if i not in zero_indexed_atom_indices_A: atom.element+='-Bq'
AB_B = copy.deepcopy(AB)
for i,atom in enumerate(AB_B):
if i in zero_indexed_atom_indices_A: atom.element+='-Bq'
#now AB_A is A from AB, AB_B is B from AB
name1 = job(AB_A, job_total+'_A0', previous_job=job_total)
name2 = job(AB_B, job_total+'_B0', previous_job=job_total)
#non-rigid correction:
AB_A = [atom for atom in AB_A if not atom.element.endswith('-Bq')]
AB_B = [atom for atom in AB_B if not atom.element.endswith('-Bq')]
name3 = job(AB_A, job_A+'_AB0', previous_job=job_A)
name4 = job(AB_B, job_B+'_AB0'+('2' if job_A==job_B else ''), previous_job=job_B)
print 'E_binding = %s - %s - %s + %s + %s - %s - %s' % (job_total, name1, name2, name3, name4, job_A, job_B)
#binding_energy_dz('pbi2_6methc_9_Imbs', 'pbi2_5methc_12_Imbs', 'methc_solv_Imbs', range (58))
#binding_energy_dz('pbcl2_3acetone_3_Cmbs', 'pbcl2_2acetone_5_Cmbs', 'acetone_1_Cmbs', range (10,23))
for job in ['pbi2_6methc_9_Imbs','pbi2_6methc_9_Imbs_A0','pbi2_6methc_9_Imbs_B0','pbi2_5methc_12_Imbs_AB0','methc_solv_Imbs_AB4','pbi2_5methc_12_Imbs','methc_solv_Imbs']:
print job,gaussian.parse_atoms(job)[0]
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 SVD(dot_size,Niter):
lattice_start = []
lattice_end = []
dot1 = [1, 2, 4, 5, 7, 9, 10]
dot4 = [4, 5, 6, 8]
for run in dot4:
# W is the optimal rotation matrix that minimizes the differences between the start and end coordinates
# read xyz file and compare the start and end structures
f = open('/fs/home/ja539/Desktop/C/jovana_test/HSEHsol_test_iter'+str(Niter)+'_'+str(run)+'_'+str(dot_size)+'.xyz')
Natoms = int(f.readline())
f.close()
atoms = filetypes.parse_xyz('/fs/home/ja539/Desktop/C/jovana_test/HSEHsol_test_iter'+str(Niter)+'_'+str(run)+'_'+str(dot_size)+'.xyz')
start_atoms = atoms[-Natoms:]
energy, end_atoms = gaussian.parse_atoms('HSEHsol_testopt4_iter'+str(Niter)+'_'+str(run)+'_'+str(dot_size),check_convergence=False)
#energy, end_atoms = gaussian.parse_atoms('/fs/home/jms875/Documents/nanocrystals/pb_oleate_hydrate/gaussian/dot2_m06_6.log',check_convergence=False)
#energy, end_atoms = gaussian.parse_atoms('gaussian/HSEHsol_core1_dot6_2.log')
startx,starty,startz,endx,endy,endz,start_com,end_com = unweighted_COM(start_atoms,end_atoms)
A = np.array([startx,starty,startz])
#print A.shape
B = np.array([endx,endy,endz])
BT = B.transpose()
C = np.dot(A,BT)
#print C.shape
U, s, V = np.linalg.svd(C, full_matrices=True)
#print U.shape, V.shape
if np.linalg.det(V) < 0:
for i in range(3):
V[2][i] = V[2][i]*-1.0
#print U.shape, V.shape
W = np.dot(V.transpose(),U.transpose())
A_new = np.dot(W,A)
# piece together an xyz file that has the end and shifted start one after the other
for i in range(len(start_atoms)):
start_atoms[i].x = A_new[0][i]
start_atoms[i].y = A_new[1][i]
start_atoms[i].z = A_new[2][i]
end_atoms[i].x = B[0][i]
end_atoms[i].y = B[1][i]
end_atoms[i].z = B[2][i]
make_xyz_file('SVD_iter'+str(Niter)+'_'+str(run)+'_'+str(dot_size), end_atoms, 'w')
make_xyz_file('SVD_iter'+str(Niter)+'_'+str(run)+'_'+str(dot_size), start_atoms, 'a')
# calculate RMS translation
D = 0.0
for a,b in zip(start_atoms,end_atoms):
D += ((a.x-b.x)*(a.x-b.x) + (a.y-b.y)*(a.y-b.y) + (a.z-b.z)*(a.z-b.z))**(0.5)
#procrustes_distance = (D/len(start_atoms))**0.5
procrustes_distance = D/len(start_atoms)
#print procrustes_distance
# relative separations
# for the core:
coreD = 0.0
for a1,b1 in zip(start_atoms[0:dot_size*2],end_atoms[0:dot_size*2]):
for a2,b2 in zip(start_atoms[0:dot_size*2],end_atoms[0:dot_size*2]):
coreD += abs(((a1.x-a2.x)*(a1.x-a2.x) + (a1.y-a2.y)*(a1.y-a2.y) + (a1.z-a2.z)*(a1.z-a2.z))**(0.5) - ((b1.x-b2.x)*(b1.x-b2.x) + (b1.y-b2.y)*(b1.y-b2.y) + (b1.z-b2.z)*(b1.z-b2.z))**(0.5))
coreD = coreD/(dot_size*2)/(dot_size*2-1)
print 'core:', coreD
# for the ligands (average over all the ligands)
ligD = [0.0]*((Natoms-2*dot_size)/10)
for i in range((Natoms-2*dot_size)/10):
for a1,b1 in zip(start_atoms[dot_size*2+10*i:dot_size*2+10*(i+1)],end_atoms[dot_size*2+10*i:dot_size*2+10*(i+1)]):
for a2,b2 in zip(start_atoms[dot_size*2+10*i:dot_size*2+10*(i+1)],end_atoms[dot_size*2+10*i:dot_size*2+10*(i+1)]):
ligD[i] += abs(((a1.x-a2.x)*(a1.x-a2.x) + (a1.y-a2.y)*(a1.y-a2.y) + (a1.z-a2.z)*(a1.z-a2.z))**(0.5) - ((b1.x-b2.x)*(b1.x-b2.x) + (b1.y-b2.y)*(b1.y-b2.y) + (b1.z-b2.z)*(b1.z-b2.z))**(0.5))
ligD[i] = ligD[i]/10/9
#print ligD
ligDavg = (sum(a for a in ligD))/len(ligD)
print 'lig:', ligDavg
allD = 0.0
for a1,b1 in zip(start_atoms,end_atoms):
for a2,b2 in zip(start_atoms,end_atoms):
allD += abs(((a1.x-a2.x)*(a1.x-a2.x) + (a1.y-a2.y)*(a1.y-a2.y) + (a1.z-a2.z)*(a1.z-a2.z))**(0.5) - ((b1.x-b2.x)*(b1.x-b2.x) + (b1.y-b2.y)*(b1.y-b2.y) + (b1.z-b2.z)*(b1.z-b2.z))**(0.5))
allD = allD/Natoms/(Natoms-1)
print 'all:', allD
for a1,b1 in zip(start_atoms[0:dot_size],end_atoms[0:dot_size]):
for a2,b2 in zip(start_atoms[dot_size:dot_size*2],end_atoms[dot_size:dot_size*2]):
lattice_start += [((a1.x-a2.x)*(a1.x-a2.x) + (a1.y-a2.y)*(a1.y-a2.y) + (a1.z-a2.z)*(a1.z-a2.z))**(0.5)]
lattice_end += [((b1.x-b2.x)*(b1.x-b2.x) + (b1.y-b2.y)*(b1.y-b2.y) + (b1.z-b2.z)*(b1.z-b2.z))**(0.5)]
def analyze_binding():
for n in [
'propanenitrile', 'butanenitrile', 'pentanenitrile',
'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2',
'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2',
'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2'
]:
contents = open('lammps/bind3_' + n + '.log').read()
opls_binding_e = float(
re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
try:
e_pair = gaussian.parse_atoms('gaussian/bind3_' + n +
'_opt1.1.log',
check_convergence=False)[0]
except:
e_pair = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt1.log',
check_convergence=False)[0]
try:
e_pair_scrf = gaussian.parse_atoms('gaussian/bind3_' + n +
'_opt2.1.log',
check_convergence=False)[0]
except:
e_pair_scrf = gaussian.parse_atoms('gaussian/bind3_' + n +
'_opt2.log',
check_convergence=False)[0]
e_single = gaussian.parse_atoms('gaussian/' + n + '_0.log')[0]
e_single_scrf = gaussian.parse_atoms('gaussian/' + n + '_1.log')[0]
try:
bsse = gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt1a.log')[0] + gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt1b.log')[0] - gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt1a_Bq.log')[0] - gaussian.parse_atoms(
'gaussian/bind3_' + n + '_opt1b_Bq.log')[0]
except:
print 1, n
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1a_Bq.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1b_Bq.log') is None
bsse = 0.0
try:
bsse_scrf = gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt2a.log')[0] + gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt2b.log')[0] - gaussian.parse_atoms(
'gaussian/bind3_' + n +
'_opt2a_Bq.log')[0] - gaussian.parse_atoms(
'gaussian/bind3_' + n + '_opt2b_Bq.log')[0]
except:
print 2, n
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2a_Bq.log') is None
#print gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2b_Bq.log') is None
bsse_scrf = 0.0
#No such file or directory: 'gaussian/bind3_aminopentane2_opt2b_Bq.log
#No such file or directory: 'gaussian/bind3_aminobutane2_opt2a_Bq.log'
#print n, opls_binding_e, e_pair, e_single, bsse, e_pair_scrf, e_single_scrf, bsse_scrf
print n, ',', opls_binding_e, ',', (
e_pair - 2 * e_single + bsse) * 627, ',', (
e_pair_scrf - 2 * e_single_scrf + bsse_scrf) * 627
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
def binding():
#for n in ['propanenitrile', 'butanenitrile', 'pentanenitrile', 'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2', 'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2', 'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2']:
for n in ['aminobutane2']:
contents = open('lammps/bind3_' + n + '.log').read()
opls_binding_e = float(
re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
atoms = filetypes.parse_xyz('bind3_' + n + '.xyz')
#opt0: use B97D
#gaussian.job(atoms, 'B97D/TZVP/Fit', 'batch', 'bind3_'+n+'_opt0', 'Opt=Cartesian', procs=1)
#opt1: use M062X
#os.system('cp gaussian/bind3_'+n+'_opt0.chk gaussian/bind3_'+n+'_opt1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1', 'Opt=Cartesian Geom=AllCheck Guess=Read', procs=1)
#opt2: M062X with solvent
#os.system('cp gaussian/bind3_'+n+'_opt0.chk gaussian/bind3_'+n+'_opt2.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2', 'Opt=Cartesian Geom=AllCheck Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
'''
jlist = subprocess.Popen('jlist', shell=True, stdout=subprocess.PIPE).communicate()[0]
if ' bind3_'+n+'_opt1 ' not in jlist and ' bind3_'+n+'_opt1.1 ' not in jlist and gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.log') is None and (not os.path.isfile('gaussian/bind3_'+n+'_opt1.1.log') or gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.1.log') is None):
os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1.1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1.1', 'Opt=Restart', procs=1)
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1.1', 'Opt=Cartesian Geom=AllCheck Guess=Read', procs=1)
print 'bind3_'+n+'_opt1.1'
if ' bind3_'+n+'_opt2 ' not in jlist and ' bind3_'+n+'_opt2.1 ' not in jlist and gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.log') is None and (not os.path.isfile('gaussian/bind3_'+n+'_opt2.1.log') or gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.1.log') is None):
os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2.1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2.1', 'Opt=Restart SCRF(Solvent=n-Hexane)', procs=1)
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2.1', 'Opt=Cartesian Geom=AllCheck Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
print 'bind3_'+n+'_opt2.1'
continue
'''
#Find BSSE without solvent (on opt1)
#os.system('cp gaussian/'+n+'_0.chk gaussian/bind3_'+n+'_opt1a.chk')
#os.system('cp gaussian/'+n+'_0.chk gaussian/bind3_'+n+'_opt1b.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1b_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.1.chk gaussian/bind3_'+n+'_opt1a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.1.chk gaussian/bind3_'+n+'_opt1b_Bq.chk')
try:
atoms = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt1.1.log',
check_convergence=False)[1]
except:
atoms = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt1.log',
check_convergence=False)[1]
#gaussian.job(atoms[ : len(atoms)/2 ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1a', 'Guess=Read', procs=1)
#gaussian.job(atoms[ len(atoms)/2 : ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1b', 'Guess=Read', procs=1)
atoms_a = copy.deepcopy(atoms)
for a in atoms_a[:len(atoms) / 2]:
a.element = a.element + '-Bq'
#gaussian.job(atoms_a, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1a_Bq', 'Guess=Read', procs=1)
for a in atoms[len(atoms) / 2:]:
a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1b_Bq', 'Guess=Read', procs=1)
#Find BSSE with solvent (on opt2)
#os.system('cp gaussian/'+n+'_1.chk gaussian/bind3_'+n+'_opt2a.chk')
#os.system('cp gaussian/'+n+'_1.chk gaussian/bind3_'+n+'_opt2b.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2b_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.1.chk gaussian/bind3_'+n+'_opt2a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.1.chk gaussian/bind3_'+n+'_opt2b_Bq.chk')
try:
atoms = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt2.1.log',
check_convergence=False)[1]
except:
atoms = gaussian.parse_atoms('gaussian/bind3_' + n + '_opt2.log',
check_convergence=False)[1]
#gaussian.job(atoms[ : len(atoms)/2 ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2a', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
#gaussian.job(atoms[ len(atoms)/2 : ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2b', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
atoms_a = copy.deepcopy(atoms)
for a in atoms_a[:len(atoms) / 2]:
a.element = a.element + '-Bq'
gaussian.job(atoms_a,
'M062X/aug-cc-pVDZ',
'batch',
'bind3_' + n + '_opt2a_Bq',
'Guess=Read SCRF(Solvent=n-Hexane)',
procs=1)
for a in atoms[len(atoms) / 2:]:
a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2b_Bq', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
continue
#atoms = atoms[ : len(atoms)/2 ]
#atoms = atoms[ len(atoms)/2 : ]
#for a in atoms[ len(atoms)/2 : ]:
# a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/cc-pVDZ', 'batch', n+'_sp4', 'SP', procs=1) #sp0 is pair, sp1,sp2 are single, sp3,sp4 with ghost atoms
os.system('cp gaussian/' + n + '_sp0.chk gaussian/' + n + '_scrf0.chk')
gaussian.job(atoms,
'M062X/aug-cc-pVDZ',
'batch',
n + '_scrf0',
'SP SCRF(Solvent=n-Hexane) Guess=Read',
procs=1) #scrf0, scrf1, scrf2
atoms1 = copy.deepcopy(atoms)
for a in atoms1[:len(atoms) / 2]:
a.element = a.element + '-Bq'
os.system('cp gaussian/' + n + '_sp0.chk gaussian/' + n + '_scrf1.chk')
gaussian.job(atoms1,
'M062X/aug-cc-pVDZ',
'batch',
n + '_scrf1',
'SP SCRF(Solvent=n-Hexane) Guess=Read',
procs=1)
atoms2 = copy.deepcopy(atoms)
for a in atoms2[len(atoms) / 2:]:
a.element = a.element + '-Bq'
os.system('cp gaussian/' + n + '_sp0.chk gaussian/' + n + '_scrf2.chk')
gaussian.job(atoms2,
'M062X/aug-cc-pVDZ',
'batch',
n + '_scrf2',
'SP SCRF(Solvent=n-Hexane) Guess=Read',
procs=1)
#pair = gaussian.parse_atoms('gaussian/'+n+'_sp0.log')[0]
#single = gaussian.parse_atoms('gaussian/'+n+'_sp1.log')[0]
#print n, opls_binding_e, 627.5*(pair - single*2)
'''
AB = gaussian.atoms(job_total)
AB_A = copy.deepcopy(AB)
for i,atom in enumerate(AB_A):
if i not in zero_indexed_atom_indices_A: atom.element+='-Bq'
AB_B = copy.deepcopy(AB)
for i,atom in enumerate(AB_B):
if i in zero_indexed_atom_indices_A: atom.element+='-Bq'
#now AB_A is A from AB, AB_B is B from AB
name1 = job(AB_A, job_total+'_A0', previous_job=job_total)
name2 = job(AB_B, job_total+'_B0', previous_job=job_total)
#non-rigid correction:
AB_A = [atom for atom in AB_A if not atom.element.endswith('-Bq')]
AB_B = [atom for atom in AB_B if not atom.element.endswith('-Bq')]
name3 = job(AB_A, job_A+'_AB0', previous_job=job_A)
name4 = job(AB_B, job_B+'_AB0'+('2' if job_A==job_B else ''), previous_job=job_B)
print 'E_binding = %s - %s - %s + %s + %s - %s - %s' % (job_total, name1, name2, name3, name4, job_A, job_B)
#binding_energy_dz('4ACN_s_4_pbcl2', 'pbcl2_3acetoN_43', 'ACN_solv', range (21))
binding_energy_dz('5_acetone_5_PbCl2', 'pbcl2_4acetone_3', 'acetone_1', range (43))
for job in []:
print job,gaussian.parse_atoms(job)[0]
def binding():
#for n in ['propanenitrile', 'butanenitrile', 'pentanenitrile', 'hexanenitrile', 'aminopropane2', 'aminobutane2', 'aminopentane2', 'aminohexane2', 'hexane2', 'methane', 'hcn2', 'cyanoacetylene2', 'acrylonitrile2', 'cyanoallene2', 'acetonitrile2', 'hc5n2']:
for n in ['aminobutane2']:
contents = open('lammps/bind3_'+n+'.log').read()
opls_binding_e = float(re.search('\n1\s+(\S+)\s+Loop time of', contents).group(1))
atoms = filetypes.parse_xyz('bind3_'+n+'.xyz')
#opt0: use B97D
#gaussian.job(atoms, 'B97D/TZVP/Fit', 'batch', 'bind3_'+n+'_opt0', 'Opt=Cartesian', procs=1)
#opt1: use M062X
#os.system('cp gaussian/bind3_'+n+'_opt0.chk gaussian/bind3_'+n+'_opt1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1', 'Opt=Cartesian Geom=AllCheck Guess=Read', procs=1)
#opt2: M062X with solvent
#os.system('cp gaussian/bind3_'+n+'_opt0.chk gaussian/bind3_'+n+'_opt2.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2', 'Opt=Cartesian Geom=AllCheck Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
'''
jlist = subprocess.Popen('jlist', shell=True, stdout=subprocess.PIPE).communicate()[0]
if ' bind3_'+n+'_opt1 ' not in jlist and ' bind3_'+n+'_opt1.1 ' not in jlist and gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.log') is None and (not os.path.isfile('gaussian/bind3_'+n+'_opt1.1.log') or gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.1.log') is None):
os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1.1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1.1', 'Opt=Restart', procs=1)
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1.1', 'Opt=Cartesian Geom=AllCheck Guess=Read', procs=1)
print 'bind3_'+n+'_opt1.1'
if ' bind3_'+n+'_opt2 ' not in jlist and ' bind3_'+n+'_opt2.1 ' not in jlist and gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.log') is None and (not os.path.isfile('gaussian/bind3_'+n+'_opt2.1.log') or gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.1.log') is None):
os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2.1.chk')
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2.1', 'Opt=Restart SCRF(Solvent=n-Hexane)', procs=1)
#gaussian.job([], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2.1', 'Opt=Cartesian Geom=AllCheck Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
print 'bind3_'+n+'_opt2.1'
continue
'''
#Find BSSE without solvent (on opt1)
#os.system('cp gaussian/'+n+'_0.chk gaussian/bind3_'+n+'_opt1a.chk')
#os.system('cp gaussian/'+n+'_0.chk gaussian/bind3_'+n+'_opt1b.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.chk gaussian/bind3_'+n+'_opt1b_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.1.chk gaussian/bind3_'+n+'_opt1a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt1.1.chk gaussian/bind3_'+n+'_opt1b_Bq.chk')
try:
atoms = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.1.log', check_convergence=False)[1]
except:
atoms = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt1.log', check_convergence=False)[1]
#gaussian.job(atoms[ : len(atoms)/2 ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1a', 'Guess=Read', procs=1)
#gaussian.job(atoms[ len(atoms)/2 : ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1b', 'Guess=Read', procs=1)
atoms_a = copy.deepcopy(atoms)
for a in atoms_a[ : len(atoms)/2 ]:
a.element = a.element + '-Bq'
#gaussian.job(atoms_a, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1a_Bq', 'Guess=Read', procs=1)
for a in atoms[ len(atoms)/2 : ]:
a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt1b_Bq', 'Guess=Read', procs=1)
#Find BSSE with solvent (on opt2)
#os.system('cp gaussian/'+n+'_1.chk gaussian/bind3_'+n+'_opt2a.chk')
#os.system('cp gaussian/'+n+'_1.chk gaussian/bind3_'+n+'_opt2b.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.chk gaussian/bind3_'+n+'_opt2b_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.1.chk gaussian/bind3_'+n+'_opt2a_Bq.chk')
#os.system('cp gaussian/bind3_'+n+'_opt2.1.chk gaussian/bind3_'+n+'_opt2b_Bq.chk')
try:
atoms = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.1.log', check_convergence=False)[1]
except:
atoms = gaussian.parse_atoms('gaussian/bind3_'+n+'_opt2.log', check_convergence=False)[1]
#gaussian.job(atoms[ : len(atoms)/2 ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2a', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
#gaussian.job(atoms[ len(atoms)/2 : ], 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2b', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
atoms_a = copy.deepcopy(atoms)
for a in atoms_a[ : len(atoms)/2 ]:
a.element = a.element + '-Bq'
gaussian.job(atoms_a, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2a_Bq', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
for a in atoms[ len(atoms)/2 : ]:
a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/aug-cc-pVDZ', 'batch', 'bind3_'+n+'_opt2b_Bq', 'Guess=Read SCRF(Solvent=n-Hexane)', procs=1)
continue
#atoms = atoms[ : len(atoms)/2 ]
#atoms = atoms[ len(atoms)/2 : ]
#for a in atoms[ len(atoms)/2 : ]:
# a.element = a.element + '-Bq'
#gaussian.job(atoms, 'M062X/cc-pVDZ', 'batch', n+'_sp4', 'SP', procs=1) #sp0 is pair, sp1,sp2 are single, sp3,sp4 with ghost atoms
os.system('cp gaussian/'+n+'_sp0.chk gaussian/'+n+'_scrf0.chk')
gaussian.job(atoms, 'M062X/aug-cc-pVDZ', 'batch', n+'_scrf0', 'SP SCRF(Solvent=n-Hexane) Guess=Read', procs=1) #scrf0, scrf1, scrf2
atoms1 = copy.deepcopy(atoms)
for a in atoms1[ : len(atoms)/2 ]:
a.element = a.element + '-Bq'
os.system('cp gaussian/'+n+'_sp0.chk gaussian/'+n+'_scrf1.chk')
gaussian.job(atoms1, 'M062X/aug-cc-pVDZ', 'batch', n+'_scrf1', 'SP SCRF(Solvent=n-Hexane) Guess=Read', procs=1)
atoms2 = copy.deepcopy(atoms)
for a in atoms2[ len(atoms)/2 : ]:
a.element = a.element + '-Bq'
os.system('cp gaussian/'+n+'_sp0.chk gaussian/'+n+'_scrf2.chk')
gaussian.job(atoms2, 'M062X/aug-cc-pVDZ', 'batch', n+'_scrf2', 'SP SCRF(Solvent=n-Hexane) Guess=Read', procs=1)
#pair = gaussian.parse_atoms('gaussian/'+n+'_sp0.log')[0]
#single = gaussian.parse_atoms('gaussian/'+n+'_sp1.log')[0]
#print n, opls_binding_e, 627.5*(pair - single*2)
'''
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