pyascec 3.0.4

This code explores the potential energy surface of atomic and molecular clusters using a modified Metropolis criterion and Markov chain. This Python implementation makes the workflow easier and more efficient.

PyASCEC

PyASCEC is a Python-based program designed to perform Markov chain simulations of atomic and molecular cluster conformations using a modified Metropolis algorithm. The acceptance criterion is based on the electronic energy of the system. During the simulation, the fragments evolve within a box centered on the center of mass of the input cluster.

For the PyASCEC program to work, you will need to have the Gaussian 09/16 (Default: g09), Dalton, or Dirac program installed. Furthermore, the PyASCEC code can likely be modified to interface with other programs.

Flux diagram for the algorithm is sketched in the following figure[2]

If you use this code please cite:

[1]> Pérez, J. F.; Restrepo, A. ASCEC V-01: Annealing Simulado Con Energı́a Cuántica. Property, Development and Implementation; Grupo de Quı́mica-Fı́sica Teórica, Instituto de Quı́mica, Universidad de Antioquia, AA 1226 Medellı́n, Colombia.

>

[2] Pérez, J. F.; Hadad, C. Z., Restrepo, A. Structural Studies of Water Tetramer. Int. J. Quantum Chem. 2008, 108, 1653.

Install

To install execute the following command

pip install pyascec

Example

Motion and rotate each one fragment of cluster

from cluster import Cluster
from ascec import *

geometry = [
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
    ]

cluster = Cluster(geometry)

# ASCEC object
obj_ascec = ASCEC(system=cluster)

# Move each
with open("move_dimer_water.xyz", "w") as f:
    for ig in range(10):
        f.write(f" {cluster.natoms} \n")
        f.write(f" Structure {ig}\n")
        seed, motion_cluster = obj_ascec.cluster.move_cluster(
            obj_ascec.cluster,
            obj_ascec.center_cube
            )
        for ifrag in motion_cluster:
            nats = len(ifrag) // 4
            for ia in range(nats):
                ia0 = ia * 4
                f.write(
                    f"{ifrag[ia0]}   {ifrag[ia0+1]}  {ifrag[ia0+2]}  {ifrag[ia0+3]}\n"
                )

Exploration of Potential Energy Surface with Gaussian

from cluster impore Cluster
from ascec import *

geometry = [
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
    ]

cluster = Cluster(
    geometry=geometry,
    ic=1,  # (1:Gaussain,2:Dalton,3:Dirac)
    alias="g09",  # alias or PATH
)

# Minimum parameters required to run ASCEC and Gaussian.
# The default methodology is HF, and the default basis set is sto-3g.
obj_ascec = ascec(cluster)

# More parameters
cluster = Cluster(
                geometry=geometry,
                ic=1,  # (1:Gaussain,2:Dalton,3:Dirac)
                alias="g09",  # alias or PATH
                meth="DFTB3LYP",
                bas="6-311G",
                nproc=2,
                mem=4.0, # Memory in GB
                )

obj_ascec = ascec(
                route=2, "1:lineal,2:geometric"
                i_temp=200, 
                n_temp=5, 
                d_temp=10, 
                max_cycles=200, 
                length=4.0,
		        seed=141423122025 # Default: minsec#day
                )

    print(" *** ASCEC Results (Gaussian) ***")
    
    # * Start exploration #####################
    energies, geoms = obj_ascec.pes_exp()
    # * End exploration   #######################

    ngeoms = len(energies)
    print(f"Total the geometries accepted: {ngeoms}")
    cc = obj_ascec.center_cube

    # * Save geometries in .xyz ##########################
    with open("dimer_water.xyz", "w") as f:
        for ic, en in enumerate(energies):
            f.write(f" {cluster.natoms} \n")
            f.write(f" Structure {ic} Energy {en} a.u.\n")
            for ifrag in geoms[ic]:
                nats = len(ifrag) // 4
                for ia in range(nats):
                    ia0 = ia * 4
                    f.write(
                        f"{ifrag[ia0]}   {ifrag[ia0+1]}  {ifrag[ia0+2]}  {ifrag[ia0+3]}\n"
                    )
            f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
            f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
            f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
            f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
            f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
            f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
            f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
            f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
    # * End  #########################################

Exploration of Potential Energy Surface with Dalton or Dirac

from cluster impore Cluster
from ascec import *

geometry = [
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
        ["O", 0.000000,  0.000000,  0.118997,
         "H", 0.000000,  0.753010, -0.475986,
         "H", 0.000000, -0.753010, -0.475986,
        ],
    ]


print(" *** ASCEC Results (Dalton) ***")
cluster = Cluster(
                    geometry=geometry,
                    ic=2,  # or (1:Gaussain,2:Dalton,3:Dirac)
                    alias="PATH/dalton",  # alias or PATH of Dalton
                    scratch="Path/scratch",  # Path of scratch
                    meth="DFTB3LYP",
                    bas="STO-3G",
                    nproc=2,
                    mem=4.0 # Memory in GB
                )

obj_ascec = ASCEC(
                    cluster,
                    i_temp=200,
                    n_temp=4,
                    d_temp=10,
                    max_cycles=50,
                    length=4.0,
                )

# * Start exploration #####################
energies, geoms = obj_ascec.pes_exp()
# * End exploration   #######################

ngeoms = len(energies)
print(f"Total the geometries accepted: {ngeoms}")
cc = obj_ascec.center_cube

# * Save geometries in .xyz ##########################
with open("dimer_water.xyz", "w") as f:
    for ic, en in enumerate(energies):
        f.write(f" {cluster.natoms} \n")
        f.write(f" Structure {ic} Energy {en} a.u.\n")
        for ifrag in geoms[ic]:
            nats = len(ifrag) // 4
            for ia in range(nats):
                ia0 = ia * 4
                f.write(
                    f"{ifrag[ia0]}   {ifrag[ia0+1]}  {ifrag[ia0+2]}  {ifrag[ia0+3]}\n"
                )
        f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
# * End  #########################################

print(" *** ASCEC Results (Dirac) ***")

cluster = Cluster(
                    geometry=geometry,
                    ic=2,  # or (1:Gaussain,2:Dalton,3:Dirac)
                    alias="PATH/pam",  # alias or PATH of Dirac
                    scratch="Path/scratch",  # Path of scratch
                    meth="DFTB3LYP",
                    bas="STO-3G",
                    nproc=2,
                    mem=4.0 # Memory in GB
                )

obj_ascec = ASCEC(
                    cluster,
                    i_temp=200,
                    n_temp=4,
                    d_temp=10,
                    max_cycles=50,
                    length=4.0,
                )


# * Start exploration #####################
energies, geoms = obj_ascec.pes_exp()
# * End exploration   #######################

ngeoms = len(energies)
print(f"Total the geometries accepted: {ngeoms}")
cc = obj_ascec.center_cube

# * Save geometries in .xyz ##########################
with open("dimer_water.xyz", "w") as f:
    for ic, en in enumerate(energies):
        f.write(f" {cluster.natoms} \n")
        f.write(f" Structure {ic} Energy {en} a.u.\n")
        for ifrag in geoms[ic]:
            nats = len(ifrag) // 4
            for ia in range(nats):
                ia0 = ia * 4
                f.write(
                    f"{ifrag[ia0]}   {ifrag[ia0+1]}  {ifrag[ia0+2]}  {ifrag[ia0+3]}\n"
                )
        f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] + 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] + 2.0}  {cc[0] - 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] + 2.0}\n")
        f.write(f"X     {cc[0] - 2.0}  {cc[0] - 2.0}  {cc[0] - 2.0}\n")
# * End  #########################################