Aspirin example

[qzhu2017]

from ost.build import Builder
from pyxtal.db import database
import numpy as np
import os

# Set the crystal model
data = [
        ('ACSALA', [[2,0,0], [0,1,0], [0,0,1]]), # Plastic, 93.99, ac
        ('ACSALA13', [[2,0,1], [0,1,0], [0,0,1]]), # Plastic, 93.99, ac
       ]

style = 'gaff'
db = database('dataset/ht.db')
#dim = [10, 10, 10]

for d in data:
    (code, matrix) = d
    matrix = np.array(matrix)
    print(code)
    xtal = db.get_pyxtal(code)
    smiles = [mol.smile for mol in xtal.molecules]
    bu = Builder(smiles=smiles, style=style)
    bu.set_xtal(xtal, para_min=5.0, dimer=True)
    # Apply the orientation

    # Directory
    folder = code+'-'+style
    if not os.path.exists(folder): os.makedirs(folder)
    cwd = os.getcwd()
    os.chdir(folder)

    # Example 1: tensile, assuming z direction
    task1 = {'type': 'tensile',
             'temperature': 200,
             'pressure': 1.0,
             'max_strain': 0.2,
             'rate': 2e+8, 
           }

    bu.set_slab(bu.xtal, bu.xtal_mol_list, matrix=matrix, dimer=True)
    print('Supercell:  ', bu.ase_slab.get_cell_lengths_and_angles())
    bu.set_task(task1)
    
    bu.lammps_slab.write_lammps()
    bu.ase_slab.write('test.xyz', format='extxyz')
    os.chdir(cwd)

[qzhu2017]

• compute VACF for dimer centers

[qzhu2017]

@pedroantoniosantosf

Below is the script to compute averaged position and velocities for each molecular center at every 1000 steps.
How can I modify the following script so that I can print out the instantaneous position and velocities for each molecular center at every 5 steps.

compute         cmol all chunk/atom molecule # Define the chunk as a molecule
compute         com all com/chunk cmol       # Calculate the center-of-mass per molecule
compute         vcm all vcm/chunk cmol       # Calculate the velocity of center-of-mass per molecule
fix             3 all ave/time 2 100 1000 c_com[*] c_vcm[*] file center.dat mode vector

[pedroantoniosantosf]

@qzhu2017

You can define each valeu as a variable and print the variables in a file:

variable       step         equal step
variable       com_x        equal c_com[1]
variable       com_y        equal c_com[2]
variable       com_z        equal c_com[3]
variable       vcm_x        equal c_vcm[1]
variable       vcm_y        equal c_vcm[2]
variable       vcm_z        equal c_vcm[3]

fix            4 all print 5 "${step} ${com_x} ${com_y} ${com_z} ${vcm_x} ${vcm_y} ${vcm_z}" file center_2.dat screen no title "# step com_x com_y com_z vcm_x vcm_y vcm_z"

[qzhu2017]

@pedroantoniosantosf

ERROR: Variable com_x: Compute global vector in equal-style variable formula (../variable.cpp:1533)

com is vector with two dimensions, [number of molecules, 3]

[qzhu2017]

@pedroantoniosantosf
I think I will just use

fix             3 all ave/time 1 1 1 c_com[*] c_vcm[*] file center.dat mode vector

[pedroantoniosantosf]

@qzhu2017
Oh, it is true. If you want to print each 5 steps, you can use:

fix             3 all ave/time 1 1 5 c_com[*] c_vcm[*] file center.dat mode vector