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SetGlobas/MolHandling(fixes)/DicePlayer Translation

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Fixed Numerus functions in the SetGlobals file and MolHandling, translated DicePlayer and tested till printing of initial geometry for cyc==1

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-09-25 15:30:40 -03:00
committed by Vitor Hideyoshi
parent 2f9cecee34
commit 316acf4761
13 changed files with 725 additions and 423 deletions
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84
DPpack/MolHandling.py
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@@ -1,4 +1,3 @@
from DPpack.MolHandling import total_mass
import os, sys
import math
import shutil
@@ -11,7 +10,11 @@ from numpy import linalg
from DPpack.Misc import *
from DPpack.PTable import *
from DPpack.SetGlobals import *
env = ["OMP_STACKSIZE"]
bohr2ang = 0.52917721092
ang2bohr = 1/bohr2ang
# Usaremos uma nova classe que ira conter toda interação entre moleculas
@@ -173,9 +176,9 @@ class System:
def print_geom(self, cycle, fh):
fh.write("{}\n".format(len(self.molecule[0])))
fh.write("{}\n".format(len(self.molecule[0].atom)))
fh.write("Cycle # {}\n".format(cycle))
for atom in self.molecule[0].atoms:
for atom in self.molecule[0].atom:
symbol = atomsymb[atom.na]
fh.write("{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(symbol,
atom.rx, atom.ry, atom.rz))
@@ -201,6 +204,8 @@ class Molecule:
self.atom.append(a) # Inserção de um novo atomo
self.total_mass += a.mass
self.center_of_mass()
def center_of_mass(self):
com = np.zeros(3)
@@ -221,9 +226,9 @@ class Molecule:
for atom in self.atom:
atom.rx -= com[0]
atom.ry -= com[1]
atom.rz -= com[2]
atom.rx -= self.com[0]
atom.ry -= self.com[1]
atom.rz -= self.com[2]
def charges_and_dipole(self):
@@ -285,15 +290,14 @@ class Molecule:
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]
dx = atom.rx - self.com[0]
dy = atom.ry - self.com[1]
dz = atom.rz - self.com[2]
#### Update the diagonal components of the tensor
Ixx += atom.mass * (dy**2 + dz**2)
Iyy += atom.mass * (dz**2 + dx**2)
@@ -332,7 +336,7 @@ class Molecule:
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) )
mat2 *= np.matmul( np.matmul(self.hessian, step.T), np.matmul(step, self.hessian) )
self.hessian += mat1 - mat2
@@ -393,10 +397,9 @@ class Molecule:
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]))
fh.write(" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )\n".format(self.com[0],
self.com[1], self.com[2]))
inertia = self.inertia_tensor()
evals, evecs = self.principal_axes()
@@ -413,60 +416,13 @@ class Molecule:
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))
fh.write(" Total mass = {:>8.2f} au\n".format(self.total_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):