Tutorial: Building Topology and Apply Forcefield parameters for Calcite

This tutorial demonstrates how to build topology for a calcite structure using known bond distances from the literature.

Prerequisites

from cemd import AtomicSystem
from cemd.topology import TopologyRule, NeighborCriterion

Step 1: Load Calcite Structure

Load the calcite structure from Tutorial: Building a Calcite (10\overline{1}4) Surface Slab from COD and understand what we’re working with.

# Load calcite structure
system = AtomicSystem.from_file("calcite_104.data")
print(system)

<AtomicSystem with 2520 atoms>

Box
a (Å)  b (Å)  c (Å)  α (°)  β (°)  γ (°)
34.86  24.36  60.89  90.00  90.00  90.00

Atoms
type  number       mass  charge
C     504 12.01078     4.0
Ca     504 40.07840     2.0
O    1512 15.99943    -2.0

Total charge: 0.000e
Volume: 51.69 nm3
Density: 1.62 g/cm3

Step 2: Create Topology Rules for Calcite

Now we create topology rules using the known bond distances.

# Carbon atom bonded to exactly 3 oxygen atoms at 1.4 Å
carbonate_topo_rule = TopologyRule(
    center="type C",
    neighbors=NeighborCriterion("type O", 1.4, 3),
    bonds=True,
    angles=True
)

print(system)

<AtomicSystem with 2520 atoms, 1512 bonds, 1512 angles>

Box
a (Å)  b (Å)  c (Å)  α (°)  β (°)  γ (°)
34.86  24.36  60.89  90.00  90.00  90.00

Atoms
type  number       mass  charge
   C     504 12.01078     4.0
  Ca     504 40.07840     2.0
   O    1512 15.99943    -2.0

Bonds
type  number
 C-O    1512

Angles
type  number
O-C-O   1512

Total charge: 0.000e
Volume: 51.69 nm3
Density: 1.62 g/cm3

Step 3: Apply Rules and Inspect Results

Apply each rule to the system and inspect the results.