Vitor Hideyoshi
a1ff35eba6
Initial work in the tradution of SetGlobals and Logistics in the use of classes for the management of processes and threaded works Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
481 lines
14 KiB
Python
481 lines
14 KiB
Python
from DPpack.MolHandling import total_mass
|
|
import os, sys
|
|
import math
|
|
import shutil
|
|
import textwrap
|
|
import sys, math
|
|
from copy import deepcopy
|
|
|
|
import numpy as np
|
|
from numpy import linalg
|
|
|
|
from DPpack.Misc import *
|
|
from DPpack.PTable import *
|
|
from DPpack.SetGlobals import *
|
|
|
|
# Usaremos uma nova classe que ira conter toda interação entre moleculas
|
|
|
|
class System:
|
|
|
|
def __init__(self):
|
|
|
|
self.molecule = []
|
|
|
|
def add_molecule(self, m):
|
|
|
|
self.molecule.append(m)
|
|
|
|
# Função que calcula a distância entre dois centros de massa
|
|
# e por se tratar de uma função de dois atomos não deve ser
|
|
# inserida dentro de Molecule
|
|
def center_of_mass_distance(self, a, b):
|
|
|
|
com1 = self.molecule[a].center_of_mass()
|
|
com2 = self.molecule[b].center_of_mass()
|
|
dx = com1[0] - com2[0]
|
|
dy = com1[1] - com2[1]
|
|
dz = com1[2] - com2[2]
|
|
distance = math.sqrt(dx**2 + dy**2 + dz**2)
|
|
|
|
return distance
|
|
|
|
def minimum_distance(self, index1, index2):
|
|
|
|
distances = []
|
|
for atom1 in self.molecule[index1]:
|
|
if atom1.na != ghost_number:
|
|
for atom2 in self.molecule[index2]:
|
|
if atom2.na != ghost_number:
|
|
dx = atom1.rx - atom2.rx
|
|
dy = atom1.ry - atom2.ry
|
|
dz = atom1.rz - atom2.rz
|
|
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
|
|
|
|
return min(distances)
|
|
|
|
def rmsd_fit(self, index_p, index_r):
|
|
|
|
projecting_mol = self.molecule[index_p]
|
|
reference_mol = self.molecule[index_r]
|
|
|
|
if len(projecting_mol.atom) != len(reference_mol.atom):
|
|
sys.exit("Error in RMSD fit procedure: molecules have different number of atoms")
|
|
dim = len(projecting_mol.atom)
|
|
|
|
new_projecting_mol = deepcopy(projecting_mol)
|
|
new_reference_mol = deepcopy(reference_mol)
|
|
|
|
new_projecting_mol.center_of_mass_to_origin()
|
|
new_reference_mol.center_of_mass_to_origin()
|
|
|
|
x = []
|
|
y = []
|
|
|
|
for atom in new_projecting_mol:
|
|
x.extend([ atom.rx, atom.ry, atom.rz ])
|
|
|
|
for atom in new_reference_mol:
|
|
y.extend([ atom.rx, atom.ry, atom.rz ])
|
|
|
|
x = np.array(x).reshape(dim, 3)
|
|
y = np.array(y).reshape(dim, 3)
|
|
|
|
r = np.matmul(y.T, x)
|
|
rr = np.matmul(r.T, r)
|
|
|
|
try:
|
|
evals, evecs = linalg.eigh(rr)
|
|
except:
|
|
sys.exit("Error: diagonalization of RR matrix did not converge")
|
|
|
|
a1 = evecs[:,2].T
|
|
a2 = evecs[:,1].T
|
|
a3 = np.cross(a1, a2)
|
|
|
|
A = np.array([ a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2] ])
|
|
A = A.reshape(3,3)
|
|
|
|
b1 = np.matmul(r, a1.T).T # or np.dot(r, a1)
|
|
b1 /= linalg.norm(b1)
|
|
b2 = np.matmul(r, a2.T).T # or np.dot(r, a2)
|
|
b2 /= linalg.norm(b2)
|
|
b3 = np.cross(b1, b2)
|
|
|
|
B = np.array([ b1[0], b1[1], b1[2], b2[0], b2[1], b2[2], b3[0], b3[1], b3[2] ])
|
|
B = B.reshape(3,3).T
|
|
|
|
rot_matrix = np.matmul(B, A)
|
|
x = np.matmul(rot_matrix, x.T).T
|
|
|
|
rmsd = 0
|
|
for i in range(dim):
|
|
rmsd += (x[i,0] - y[i,0])**2 + (x[i,1] - y[i,1])**2 + (x[i,2] - y[i,2])**2
|
|
rmsd = math.sqrt(rmsd/dim)
|
|
|
|
for i in range(dim):
|
|
new_projecting_mol.atom[i].rx = x[i,0]
|
|
new_projecting_mol.atom[i].ry = x[i,1]
|
|
new_projecting_mol.atom[i].rz = x[i,2]
|
|
|
|
tr_vector = reference_mol.center_of_mass()
|
|
projected_mol = new_projecting_mol.translate(tr_vector)
|
|
|
|
return rmsd, projected_mol
|
|
|
|
def update_molecule(self, position, fh):
|
|
|
|
position_in_ang = (position * bohr2ang).tolist()
|
|
self.add_molecule(deepcopy(self.molecule[0]))
|
|
|
|
for atom in self.molecule[-1].atom:
|
|
|
|
atom.rx = position_in_ang.pop(0)
|
|
atom.ry = position_in_ang.pop(0)
|
|
atom.rz = position_in_ang.pop(0)
|
|
|
|
rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
|
|
self.molecule.pop(-1)
|
|
|
|
fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
|
|
fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
|
|
|
|
def nearest_image(self, index_r, index_m, lx, ly, lz, criterium=None):
|
|
|
|
if criterium in None:
|
|
criterium = "com"
|
|
|
|
if criterium != "com" and criterium != "min":
|
|
sys.exit("Error in value passed to function nearest_image")
|
|
|
|
min_dist = 1e20
|
|
|
|
for i in range(-1, 2):
|
|
for j in range(-1, 2):
|
|
for k in range(-1, 2):
|
|
|
|
tr_vector = [i * lx, j * ly, k * lz]
|
|
self.add_molecule(self.molecule[index_m].translate(tr_vector))
|
|
|
|
if criterium == "com":
|
|
dist = self.center_of_mass_distance(index_r, -1)
|
|
else:
|
|
dist = self.minimum_distance(index_r, -1)
|
|
|
|
if dist < min_dist:
|
|
min_dist = dist
|
|
nearestmol = deepcopy(self.molecule[-1])
|
|
|
|
self.molecule.pop(-1)
|
|
|
|
return min_dist, nearestmol
|
|
|
|
def print_geom(self, cycle, fh):
|
|
|
|
fh.write("{}\n".format(len(self.molecule[0])))
|
|
fh.write("Cycle # {}\n".format(cycle))
|
|
for atom in self.molecule[0].atoms:
|
|
symbol = atomsymb[atom.na]
|
|
fh.write("{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(symbol,
|
|
atom.rx, atom.ry, atom.rz))
|
|
|
|
|
|
|
|
# Classe que conterá toda informação e funções relacionadas a uma unica molecula
|
|
|
|
class Molecule:
|
|
|
|
def __init__(self):
|
|
|
|
self.atom = [] # Lista de instancias de Atom
|
|
self.position = None # Array Numpy
|
|
self.energy = None # Array Numpy
|
|
self.gradient = None # Array Numpy
|
|
self.hessian = None # Array Numpy
|
|
self.total_mass = 0
|
|
|
|
def add_atom(self, a):
|
|
|
|
self.atom.append(a) # Inserção de um novo atomo
|
|
self.total_mass += a.mass
|
|
|
|
def center_of_mass(self):
|
|
|
|
com = np.zeros(3)
|
|
total_mass = 0.0
|
|
|
|
for atom in self.atom:
|
|
|
|
total_mass += atom.mass
|
|
com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
|
|
|
|
com = com / total_mass
|
|
|
|
return com
|
|
|
|
def center_of_mass_to_origin(self):
|
|
|
|
com = self.center_of_mass()
|
|
|
|
for atom in self.atom:
|
|
|
|
atom.rx -= com[0]
|
|
atom.ry -= com[1]
|
|
atom.rz -= com[2]
|
|
|
|
def charges_and_dipole(self):
|
|
|
|
eA_to_Debye = 1/0.20819434
|
|
charge = 0
|
|
dipole = np.zeros(3)
|
|
for atom in self.atom:
|
|
position = np.array([ atom.rx, atom.ry, atom.rz ])
|
|
dipole += atom.chg * position
|
|
charge += atom.chg
|
|
|
|
dipole *= eA_to_Debye
|
|
total_dipole = math.sqrt(dipole[0]**2 + dipole[1]**2 + dipole[2]**2)
|
|
|
|
return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
|
|
|
|
def distances_between_atoms(self):
|
|
|
|
distances = []
|
|
dim = len(self.atom)
|
|
for atom1 in self.atom:
|
|
if atom1.na != ghost_number:
|
|
for atom2 in self.atom:
|
|
if atom2.na != ghost_number:
|
|
dx = atom1.rx - atom2.rx
|
|
dy = atom1.ry - atom2.ry
|
|
dz = atom1.rz - atom2.rz
|
|
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
|
|
|
|
return np.array(distances).reshape(dim, dim)
|
|
|
|
def eixos(self):
|
|
|
|
eixos = np.zeros(3)
|
|
if len(self.atom) == 2:
|
|
|
|
position1 = np.array([ self.atom[0].rx, self.atom[0].ry, self.atom[0].rz ])
|
|
position2 = np.array([ self.atom[1].rx, self.atom[1].ry, self.atom[1].rz ])
|
|
eixos = position2 - position1
|
|
eixos /= linalg.norm(eixos)
|
|
|
|
elif len(self.atom) > 2:
|
|
|
|
position1 = np.array([ self.atom[0].rx, self.atom[0].ry, self.atom[0].rz ])
|
|
position2 = np.array([ self.atom[1].rx, self.atom[1].ry, self.atom[1].rz ])
|
|
position3 = np.array([ self.atom[2].rx, self.atom[2].ry, self.atom[2].rz ])
|
|
v1 = position2 - position1
|
|
v2 = position3 - position1
|
|
v3 = np.cross(v1, v2)
|
|
v2 = np.cross(v1, v3)
|
|
v1 /= linalg.norm(v1)
|
|
v2 /= linalg.norm(v2)
|
|
v3 /= linalg.norm(v3)
|
|
eixos = np.array([[v1[0], v1[1], v1[2]],
|
|
[v2[0], v2[1], v2[2]],
|
|
[v3[0], v3[1], v3[2]]])
|
|
|
|
return eixos
|
|
|
|
def inertia_tensor(self):
|
|
|
|
com = self.center_of_mass()
|
|
Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
|
|
|
|
for atom in self.atom:
|
|
|
|
#### Obtain the displacement from the center of mass
|
|
dx = atom.rx - com[0]
|
|
dy = atom.ry - com[1]
|
|
dz = atom.rz - com[2]
|
|
#### Update the diagonal components of the tensor
|
|
Ixx += atom.mass * (dy**2 + dz**2)
|
|
Iyy += atom.mass * (dz**2 + dx**2)
|
|
Izz += atom.mass * (dx**2 + dy**2)
|
|
#### Update the off-diagonal components of the tensor
|
|
Ixy += atom.mass * dx * dy * -1
|
|
Ixz += atom.mass * dx * dz * -1
|
|
Iyz += atom.mass * dy * dz * -1
|
|
|
|
return np.array([ [Ixx, Ixy, Ixz],
|
|
[Ixy, Iyy, Iyz],
|
|
[Ixz, Iyz, Izz] ])
|
|
|
|
def principal_axes(self):
|
|
|
|
try:
|
|
evals, evecs = linalg.eigh(self.inertia_tensor())
|
|
except:
|
|
sys.exit("Error: diagonalization of inertia tensor did not converge")
|
|
|
|
return evals, evecs
|
|
|
|
def read_position(self):
|
|
|
|
position_list = []
|
|
for atom in self.atom:
|
|
position_list.extend([ atom.rx, atom.ry, atom.rz ])
|
|
position = np.array(position_list)
|
|
position *= ang2bohr
|
|
|
|
return position
|
|
|
|
def update_hessian(self, step, cur_gradient): ## According to the BFGS
|
|
|
|
dif_gradient = cur_gradient - self.gradient
|
|
|
|
mat1 = 1/np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient)
|
|
mat2 = 1/np.dot(step, np.matmul(self.hessian, step.T).T)
|
|
mat2 *= np.matmul( np.matmul(self.hessian, step.T), np.matmul(step, hessian) )
|
|
|
|
self.hessian += mat1 - mat2
|
|
|
|
def sizes_of_molecule(self):
|
|
|
|
x_list = []
|
|
y_list = []
|
|
z_list = []
|
|
|
|
for atom in self.atom:
|
|
if atom.na != ghost_number:
|
|
x_list.append(atom.rx)
|
|
y_list.append(atom.ry)
|
|
z_list.append(atom.rz)
|
|
|
|
x_max = max(x_list)
|
|
x_min = min(x_list)
|
|
y_max = max(y_list)
|
|
y_min = min(y_list)
|
|
z_max = max(z_list)
|
|
z_min = min(z_list)
|
|
|
|
sizes = [x_max - x_min, y_max - y_min, z_max - z_min]
|
|
|
|
return sizes
|
|
|
|
def standard_orientation(self):
|
|
|
|
self.center_of_mass_to_origin()
|
|
tensor = self.inertia_tensor()
|
|
evals, evecs = self.principal_axes()
|
|
|
|
if round(linalg.det(evecs)) == -1:
|
|
evecs[0,2] *= -1
|
|
evecs[1,2] *= -1
|
|
evecs[2,2] *= -1
|
|
if round(linalg.det(evecs)) != 1:
|
|
sys.exit("Error: could not make a rotation matrix while adopting the standard orientation")
|
|
|
|
rot_matrix = evecs.T
|
|
for atom in self.atom:
|
|
position = np.array([ atom.rx, atom.ry, atom.rz ])
|
|
new_position = np.matmul(rot_matrix, position.T).T
|
|
atom.rx = new_position[0]
|
|
atom.ry = new_position[1]
|
|
atom.rz = new_position[2]
|
|
|
|
def translate(self, vector):
|
|
|
|
new_molecule = deepcopy(self)
|
|
|
|
for atom in new_molecule.atom:
|
|
|
|
atom.rx += vector[0]
|
|
atom.ry += vector[1]
|
|
atom.rz += vector[2]
|
|
|
|
return new_molecule
|
|
|
|
def print_mol_info(self, fh):
|
|
|
|
com = self.center_of_mass()
|
|
fh.write(" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )\n".format(com[0],
|
|
com[1], com[2]))
|
|
inertia = self.inertia_tensor()
|
|
evals, evecs = self.principal_axes()
|
|
|
|
fh.write(" Moments of inertia = {:>9E} {:>9E} {:>9E}\n".format(evals[0],
|
|
evals[1], evals[2]))
|
|
|
|
fh.write(" Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
|
evecs[0,0], evecs[1,0], evecs[2,0]))
|
|
fh.write(" Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
|
evecs[0,1], evecs[1,1], evecs[2,1]))
|
|
fh.write(" Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
|
evecs[0,2], evecs[1,2], evecs[2,2]))
|
|
|
|
sizes = self.sizes_of_molecule()
|
|
fh.write(" Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )\n".format(
|
|
sizes[0], sizes[1], sizes[2]))
|
|
mol_mass = self.total_mass()
|
|
fh.write(" Total mass = {:>8.2f} au\n".format(mol_mass))
|
|
|
|
chg_dip = self.charges_and_dipole()
|
|
fh.write(" Total charge = {:>8.4f} e\n".format(chg_dip[0]))
|
|
fh.write(" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye\n\n".format(
|
|
chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]))
|
|
|
|
def calculate_step(self, fh):
|
|
|
|
invhessian = linalg.inv(self.hessian)
|
|
pre_step = -1 * np.matmul(invhessian, self.gradient.T).T
|
|
maxstep = np.amax(np.absolute(pre_step))
|
|
factor = min(1, player['maxstep']/maxstep)
|
|
step = factor * pre_step
|
|
|
|
fh.write("\nCalculated step:\n")
|
|
pre_step_list = pre_step.tolist()
|
|
|
|
fh.write("-----------------------------------------------------------------------\n"
|
|
"Center Atomic Step (Bohr)\n"
|
|
"Number Number X Y Z\n"
|
|
"-----------------------------------------------------------------------\n")
|
|
for i in range(len(molecules[0])):
|
|
fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
|
i + 1, molecules[0][i]['na'],
|
|
pre_step_list.pop(0), pre_step_list.pop(0), pre_step_list.pop(0)))
|
|
|
|
fh.write("-----------------------------------------------------------------------\n")
|
|
|
|
fh.write("Maximum step is {:>11.6}\n".format(maxstep))
|
|
fh.write("Scaling factor = {:>6.4f}\n".format(factor))
|
|
fh.write("\nFinal step (Bohr):\n")
|
|
step_list = step.tolist()
|
|
|
|
fh.write("-----------------------------------------------------------------------\n"
|
|
"Center Atomic Step (Bohr)\n"
|
|
"Number Number X Y Z\n"
|
|
"-----------------------------------------------------------------------\n")
|
|
for i in range(len(molecules[0])):
|
|
fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
|
i + 1, molecules[0][i]['na'],
|
|
step_list.pop(0), step_list.pop(0), step_list.pop(0)))
|
|
|
|
fh.write("-----------------------------------------------------------------------\n")
|
|
|
|
step_max = np.amax(np.absolute(step))
|
|
step_rms = np.sqrt(np.mean(np.square(step)))
|
|
|
|
fh.write(" Max Step = {:>14.9f} RMS Step = {:>14.9f}\n\n".format(
|
|
step_max, step_rms))
|
|
|
|
return step
|
|
|
|
class Atom:
|
|
|
|
def __init__(self, lbl,na,rx,ry,rz,chg,eps,sig):
|
|
|
|
self.lbl = lbl # Integer
|
|
self.na = na # Integer
|
|
self.rx = rx # Double
|
|
self.ry = ry # Double
|
|
self.rz = rz # Double
|
|
self.chg = chg # Double
|
|
self.eps = eps # Double
|
|
self.sig = sig # Double
|
|
self.mass = atommass[self.na] # Double
|
|
|