`add_spring`

This keyword adds spring interactions to selected atom groups at each step of a run.

It supports three modes: ghost_com, ghost_atom, and com_com, which add spring forces between a ghost atom and the center of mass (COM) of a group, between ghost atoms and their corresponding atoms in a group, and between the COMs of two groups, respectively. The ghost atom(s) can be static or move at a constant velocity. Each mode supports two spring types: couple (a single radial spring) and decouple (three independent springs along the x, y, and z directions).

Syntax

The complete syntax for the six combinations is:

add_spring ghost_com <group_method> <group_id> <ghost_vx> <ghost_vy> <ghost_vz> couple <k_couple> <R0> <offset_x> <offset_y> <offset_z>
add_spring ghost_com <group_method> <group_id> <ghost_vx> <ghost_vy> <ghost_vz> decouple <k_decouple_x> <k_decouple_y> <k_decouple_z> <offset_x> <offset_y> <offset_z>
add_spring ghost_atom <group_method> <group_id> <ghost_vx> <ghost_vy> <ghost_vz> couple <k_couple> <R0> <offset_x> <offset_y> <offset_z>
add_spring ghost_atom <group_method> <group_id> <ghost_vx> <ghost_vy> <ghost_vz> decouple <k_decouple_x> <k_decouple_y> <k_decouple_z> <offset_x> <offset_y> <offset_z>
add_spring com_com <group_method> <group_id_1> <group_id_2> couple <k_couple> <R0>
add_spring com_com <group_method> <group_id_1> <group_id_2> decouple <k_decouple_x> <k_decouple_y> <k_decouple_z>

The coupled spring potential is:

\[U_{\mathrm{couple}} = \frac{1}{2} k_{\mathrm{couple}} (R - R_0)^2\]

where \(R\) is the distance between the two points connected by the spring.

The decoupled spring potential is:

\[U_{\mathrm{decouple}} = \frac{1}{2} k_{\mathrm{decouple},x} (x_2 - x_1)^2 + \frac{1}{2} k_{\mathrm{decouple},y} (y_2 - y_1)^2 + \frac{1}{2} k_{\mathrm{decouple},z} (z_2 - z_1)^2\]

where \((x_1, y_1, z_1)\) and \((x_2, y_2, z_2)\) are the Cartesian coordinates of the two points connected by the spring.

In ghost_com mode, force is added to atoms in group group_id of group method group_method with mass-weighted distribution. The ghost is initially placed at the COM + (offset_x, offset_y, offset_z) and is displaced by (ghost_vx, ghost_vy, ghost_vz) at each step.
In ghost_atom mode, each atom in group group_id is attached to its own ghost anchor. The anchor is initially placed at the atom position + (offset_x, offset_y, offset_z) and is displaced by (ghost_vx, ghost_vy, ghost_vz) at each step. The input spring constant(s) (k_couple or k_decouple_x, k_decouple_y, k_decouple_z) represent the total stiffness of the entire group and are divided internally by the number of atoms in the group. Thus, each atom experiences a spring with an effective stiffness of k / N_atoms.
In com_com mode, a spring interaction is applied between the COM of group group_id_1 and the COM of group group_id_2 under the same group_method. Equal and opposite forces are applied to the two groups with mass-weighted distribution within each group.
In couple mode, k_couple must be positive and R0 must be non-negative.
In decouple mode, k_decouple_x, k_decouple_y, and k_decouple_z must be non-negative.
In com_com mode, group_id_1 and group_id_2 must be different.
Force is in units of eV/Å, distance is in units of Å, velocity is in units of Å/step, and spring constant is in units of eV/Å².
Spring forces are written to the file spring_force_*.out, where the asterisk is replaced by a zero-based index that increments with each invocation of the command. The meaning of each column in the file is:
```
# step  mode  Fx  Fy  Fz  Ftotal  energy
```

where mode is an integer flag: 0 = ghost_com, 1 = ghost_atom, 2 = com_com. In com_com mode, the reported Fx, Fy, and Fz correspond to the net spring force applied to group_id_1.

Example 1 (ghost_com + couple)

Add a coupled spring with spring constant 10 eV/Å² and equilibrium distance 0 Å between a static ghost atom and the COM of atoms in group 2 defined by group method 0. The ghost atom is initially located at the COM:

add_spring ghost_com 0 2 0 0 0 couple 10 0 0 0 0

Example 2 (ghost_com + decouple)

Add a decoupled spring with spring constants 10 eV/Å² in the x direction and 0 eV/Å² in the y and z directions between a ghost atom moving at velocity (0.00005, 0, 0) Å/step and the COM of atoms in group 2 defined by group method 0. The ghost atom is initially located at the COM:

add_spring ghost_com 0 2 0.00005 0 0 decouple 10 0 0 0 0 0

Example 3 (ghost_atom + couple)

Add a coupled spring between each atom in group 2 defined by group method 0 and its corresponding moving ghost anchor. Each anchor is initially placed at the corresponding atom position and moves at velocity (0.00005, 0, 0) Å/step:

add_spring ghost_atom 0 2 0.00005 0 0 couple 10 0 0 0 0

Example 4 (com_com + decouple)

Add a decoupled Cartesian spring between the COM of group 1 and the COM of group 2 under the same group method 0:

add_spring com_com 0 1 2 decouple 10 0 0

Note

This keyword can be used multiple times during a run.

add_spring